Re: [Freesurfer] [EXT] Re: PetSurfer Crashing {Disarmed}
External Email - Use Caution My mistake, I think that fixed it. Thank you! Anna From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve Sent: Monday, July 20, 2020 11:45 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] PetSurfer Crashing Did you really mean to pass subject/mri/gtmseg.lta ? The registration is supposed to be the registration of the input (PET.template.nii.gz) to the anatomical. subject/mri/gtmseg.lta is the registration of gtmseg.mgz to the anatomical. On 7/20/20 11:21 AM, Crawford, Anna wrote: External Email - Use Caution Hello, I am trying to run the PetSurfer process for the first time. I was able to run gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc, it is crashing, but I am not sure why. The command I am using and output are below. Do you have any guidance as to what is going wrong? Thank you, Anna mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o subject/gtmpvc.output Loading input ../CTPET/PET.template.nii.gz done loading input 1 frames $Id: mri_gtmpvc.c,v 1.69.2.1<http://1.69.2.1> 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/ cd /mnt/autofs/netRAID18/7T/study709/S2sdt mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o subject/gtmpvc.output sysname Linux hostname fmri15 machine x86_64 user crawforda vgthresh 0.001000 nReplace 18 0. 0. 0. 0. 0. 0. 20 avail.processors, using 1 Creating output directory subject/gtmpvc.output Loading seg for gtm subject/mri/gtmseg.mgz Loading seg ctab subject/mri/gtmseg.ctab Reading subject/mri/gtmseg.lta Replacing 18 Pruning ctab Checking tissue type done with seg vol maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10 Computing auto mask Automask, reducing FOV region 256 256 109 reduced to 21 11 3 235 245 106 ERROR: LTAconcat(): LTAs 0 and 1 do not match LTA 0 --- type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0. 0. 0. sigma = 1. 1 4 4 9.97615814209e-01 0.000e+00 -8.381903171539307e-09 -7.62939453125e-06 7.450580596923828e-09 9.98807907104e-01 0.000e+00 0.000e+00 -7.450580596923828e-09 7.450580596923828e-09 9.98211860657e-01 -1.52587890625e-05 0.000e+00 0.000e+00 0.000e+00 9.99403953552e-01 src volume info valid = 1 # volume info valid filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz volume = 256 256 256 voxelsize = 1.000e+00 1.000e+00 1.000e+00 xras = -1.000e+00 0.000e+00 0.000e+00 yras = 0.000e+00 0.000e+00 -1.000e+00 zras = 0.000e+00 1.000e+00 0.000e+00 cras = 4.125e+00 3.554792785644531e+01 -2.000e+01 dst volume info valid = 1 # volume info valid filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz volume = 256 256 256 voxelsize = 1.000e+00 1.000e+00 1.000e+00 xras = -1.000e+00 0.000e+00 0.000e+00 yras = 0.000e+00 0.000e+00 -1.000e+00 zras = 0.000e+00 1.000e+00 0.000e+00 cras = 4.125e+00 3.554792785644531e+01 -2.000e+01 subject subject fscale 0.15 LTA 1 --- type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0. 0. 0. sigma = 1. 1 4 4 9.99403953552e-01 0.000e+00 0.000e+00 -2.09237060547e+01 0.000e+00 9.99403953552e-01 0.000e+00 -1.10762939453e+01 0.000e+00 0.000e+00 1.000e+00 -3.000e+00 0.000e+00 0.000e+00 0.000e+00 1.000e+00 src volume info valid = 1 # volume info valid filename = ../CTPET/PET.template.nii.gz volume = 256 256 109 voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.02971389771e+00 xras = -1.000e+00 -0.000e+00 0.000e+00 yras = -0.000e+00 1.000e+00 0.000e+00 zras = -0.000e+00 -0.000e+00 1.000e+00 cras = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03 dst volume info valid = 1 # volume info valid filename = volume = 235 245 106 voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.02971389771e+00 xras = -1.000e+00 -0.000e+00 0.0
[Freesurfer] PetSurfer Crashing
External Email - Use Caution Hello, I am trying to run the PetSurfer process for the first time. I was able to run gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc, it is crashing, but I am not sure why. The command I am using and output are below. Do you have any guidance as to what is going wrong? Thank you, Anna mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o subject/gtmpvc.output Loading input ../CTPET/PET.template.nii.gz done loading input 1 frames $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/ cd /mnt/autofs/netRAID18/7T/study709/S2sdt mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o subject/gtmpvc.output sysname Linux hostname fmri15 machine x86_64 user crawforda vgthresh 0.001000 nReplace 18 0. 0. 0. 0. 0. 0. 20 avail.processors, using 1 Creating output directory subject/gtmpvc.output Loading seg for gtm subject/mri/gtmseg.mgz Loading seg ctab subject/mri/gtmseg.ctab Reading subject/mri/gtmseg.lta Replacing 18 Pruning ctab Checking tissue type done with seg vol maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10 Computing auto mask Automask, reducing FOV region 256 256 109 reduced to 21 11 3 235 245 106 ERROR: LTAconcat(): LTAs 0 and 1 do not match LTA 0 --- type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0. 0. 0. sigma = 1. 1 4 4 9.97615814209e-01 0.000e+00 -8.381903171539307e-09 -7.62939453125e-06 7.450580596923828e-09 9.98807907104e-01 0.000e+00 0.000e+00 -7.450580596923828e-09 7.450580596923828e-09 9.98211860657e-01 -1.52587890625e-05 0.000e+00 0.000e+00 0.000e+00 9.99403953552e-01 src volume info valid = 1 # volume info valid filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz volume = 256 256 256 voxelsize = 1.000e+00 1.000e+00 1.000e+00 xras = -1.000e+00 0.000e+00 0.000e+00 yras = 0.000e+00 0.000e+00 -1.000e+00 zras = 0.000e+00 1.000e+00 0.000e+00 cras = 4.125e+00 3.554792785644531e+01 -2.000e+01 dst volume info valid = 1 # volume info valid filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz volume = 256 256 256 voxelsize = 1.000e+00 1.000e+00 1.000e+00 xras = -1.000e+00 0.000e+00 0.000e+00 yras = 0.000e+00 0.000e+00 -1.000e+00 zras = 0.000e+00 1.000e+00 0.000e+00 cras = 4.125e+00 3.554792785644531e+01 -2.000e+01 subject subject fscale 0.15 LTA 1 --- type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0. 0. 0. sigma = 1. 1 4 4 9.99403953552e-01 0.000e+00 0.000e+00 -2.09237060547e+01 0.000e+00 9.99403953552e-01 0.000e+00 -1.10762939453e+01 0.000e+00 0.000e+00 1.000e+00 -3.000e+00 0.000e+00 0.000e+00 0.000e+00 1.000e+00 src volume info valid = 1 # volume info valid filename = ../CTPET/PET.template.nii.gz volume = 256 256 109 voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.02971389771e+00 xras = -1.000e+00 -0.000e+00 0.000e+00 yras = -0.000e+00 1.000e+00 0.000e+00 zras = -0.000e+00 -0.000e+00 1.000e+00 cras = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03 dst volume info valid = 1 # volume info valid filename = volume = 235 245 106 voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.02971389771e+00 xras = -1.000e+00 -0.000e+00 0.000e+00 yras = -0.000e+00 1.000e+00 0.000e+00 zras = -0.000e+00 -0.000e+00 1.000e+00 cras = -1.861288452148438e+01 1.840597229003906e+02 1.250690063476562e+03 -- Data load time 10.9 sec nmask = 3714389, nsegs = 100, excluding segid=0 FWHM: 6 6 6 Std: 2.54797 2.54797 2.54797 nPad 10, PadThresh 0.0001 Checking Ref Ids Segmentations used for rescaling 174 Pons Computing Seg PVF Segmentation fault (core dumped) Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in
Re: [Freesurfer] [EXT] Re: Thalamic subnuclei color table
External Email - Use Caution Thank you! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lilla Zollei Sent: Friday, October 25, 2019 8:41 AM To: Freesurfer support list Subject: [EXT] Re: [Freesurfer] Thalamic subnuclei color table Hi Anna, See attached. Lilla On Fri, 25 Oct 2019, Crawford, Anna wrote: > > External Email - Use Caution > > Hello, > > > Just a quick question. We recently installed the new thalamus segmentation > subroutine. It's really wonderful, and much promise to our work. > > I can't find a lookup table with the numerical labels from the FS output to > the thalamic nuclei. The numbers around between 8103-8133 on the right, and > 8203 and 8233 on the left. Can you point me in the right direction for this? > > For other FS segmented volumes I always use the following, but it doesn't > include these thalamic subnuclei > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT> > > Thank you, > Anna > > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is currently ranked as one of the nation's top hospitals by > U.S. News & World Report (2019-2020). Visit us online at > http://www.clevelandclinic.org<http://www.clevelandclinic.org> for a complete > listing of our services, staff and locations. Confidentiality Note: This > message is intended for use only by the individual or entity > to which it is addressed and may contain information that is privileged, > confidential, and exempt from disclosure under applicable law. If the reader > of this message is not the intended recipient or the employee or agent > responsible for delivering the message to the intended recipient, you are > hereby notified > that any dissemination, distribution or copying of this communication is > strictly prohibited. If you have received this communication in error, please > contact the sender immediately and destroy the material in its entirety, > whether electronic or hard copy. Thank you. > Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thalamic subnuclei color table
External Email - Use Caution Hello, Just a quick question. We recently installed the new thalamus segmentation subroutine. It's really wonderful, and much promise to our work. I can't find a lookup table with the numerical labels from the FS output to the thalamic nuclei. The numbers around between 8103-8133 on the right, and 8203 and 8233 on the left. Can you point me in the right direction for this? For other FS segmented volumes I always use the following, but it doesn't include these thalamic subnuclei http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT Thank you, Anna Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] [EXT] Re: 1.5T Infant Brain Analysis
External Email - Use Caution Hi Lilla, Good to know. Thank you for the reply! Anna From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lilla Zollei Sent: Thursday, April 11, 2019 10:46 AM To: Freesurfer support list Subject: [EXT] Re: [Freesurfer] 1.5T Infant Brain Analysis Hi Anna, We have not tried the pipeline on 1.5T data, but you are welcome to download the beta version and see how well it is doing. https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS<https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS> Lilla On Thu, 11 Apr 2019, Crawford, Anna wrote: > > Hello, > > > I was looking to use the Freesurfer infant brains pipeline. I have found it > used with 3T data, but I was wondering if it can be used with 1.5T data as > well. > > > Thanks, > > Anna > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is currently ranked as the No. 2 hospital in the country by > U.S. News & World Report (2018-2019). Visit us online at > http://www.clevelandclinic.org<http://www.clevelandclinic.org> for a complete > listing of our services, staff and locations. Confidentiality Note: This > message is intended for use only by the individual or entity > to which it is addressed and may contain information that is privileged, > confidential, and exempt from disclosure under applicable law. If the reader > of this message is not the intended recipient or the employee or agent > responsible for delivering the message to the intended recipient, you are > hereby notified > that any dissemination, distribution or copying of this communication is > strictly prohibited. If you have received this communication in error, please > contact the sender immediately and destroy the material in its entirety, > whether electronic or hard copy. Thank you. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 1.5T Infant Brain Analysis
External Email - Use Caution Hello, I was looking to use the Freesurfer infant brains pipeline. I have found it used with 3T data, but I was wondering if it can be used with 1.5T data as well. Thanks, Anna Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: Re: Re: Re: Re: Time Series to Surface
What do I put for the email to send to? freesurfer@nmr.mgh.harvard.edu and freesurfer-boun...@nmr.mgh.harvard.edu said it was not a valid account From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu> Sent: Friday, April 6, 2018 12:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Re: Re: Time Series to Surface Can you upload the volume (img and hdr) here: https://gate.nmr.mgh.harvard.edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> On 4/6/18 12:24 PM, Crawford, Anna wrote: 1227 frames Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Friday, April 6, 2018 12:14 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXT] Re: [Freesurfer] Re: Re: Re: Time Series to Surface How many frames are in your input file? Eg, if you run mri_info on it? On 4/6/18 12:05 PM, Crawford, Anna wrote: I just opened freeview and loaded everything in the GUI. I did not use the command line to open it. I do not see a slider bar. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Friday, April 6, 2018 11:54 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXT] Re: [Freesurfer] Re: Re: Time Series to Surface what is your freeview command line? Do you see a "frame" slider bar? On 4/6/18 10:46 AM, Crawford, Anna wrote: I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, but I am still not able to view the time course. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Friday, April 6, 2018 10:21 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon (unless you specifically want to sample on the gray/white border) On 4/6/18 10:11 AM, Crawford, Anna wrote: Hello, I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere? bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5 mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXT] Re: [Freesurfer] Time Series to Surface Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview On 04/05/2018 01:49 PM, Crawford, Anna wrote: Hello, I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume? Thanks for your help, Anna === Please consider the environ
Re: [Freesurfer] Re: Re: Re: Re: Time Series to Surface
1227 frames Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu> Sent: Friday, April 6, 2018 12:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Re: Time Series to Surface How many frames are in your input file? Eg, if you run mri_info on it? On 4/6/18 12:05 PM, Crawford, Anna wrote: > I just opened freeview and loaded everything in the GUI. I did not use the > command line to open it. I do not see a slider bar. > > Thanks, > Anna > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve > <dgr...@mgh.harvard.edu> > Sent: Friday, April 6, 2018 11:54 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [EXT] Re: [Freesurfer] Re: Re: Time Series to Surface > > what is your freeview command line? Do you see a "frame" slider bar? > > > On 4/6/18 10:46 AM, Crawford, Anna wrote: >> I tried without --init-fsl and adding in the --projfrac 0.5 for >> mri_vol2surf, but I am still not able to view the time course. >> >> Thanks, >> Anna >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve >> <dgr...@mgh.harvard.edu> >> Sent: Friday, April 6, 2018 10:21 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface >> >> No need to use --init-fsl (if using version 6). For mri_vol2surf add >> --projfrac 0.5 to sample in the middle of the ribbon (unless you >> specifically want to sample on the gray/white border) >> >> >> On 4/6/18 10:11 AM, Crawford, Anna wrote: >>> Hello, >>> >>> I used the following commands and then opened the surface as an overlay on >>> the inflated volume, but I am not about to look at the time series. The >>> view time course is grayed out so that I can not click on it. Did I miss a >>> step or lose the actual time series somewhere? >>> >>> bbregister --s S2sdt/subject/ --mov >>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr >>> --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5 >>> >>> mri_vol2surf --src >>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr >>> --out >>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz >>> --srcreg >>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat >>> --hemi lh >>> >>> >>> Thank you, >>> Anna >>> >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve >>> <dgr...@mgh.harvard.edu> >>> Sent: Thursday, April 5, 2018 5:29 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: [EXT] Re: [Freesurfer] Time Series to Surface >>> >>> Use bbregister. Run with --help to get docs (make sure to use --projfrac >>> 0.5). Once you have it on the surface, you can step through each frame >>> in freeview >>> >>> >>> On 04/05/2018 01:49 PM, Crawford, Anna wrote: >>>> Hello, >>>> >>>> I have a time series (.hdr/.img) that I want to overlay onto a >>>> surface, specifically the inflated surface from the anatomy. I suspect >>>> I have to use mri_vol2surf, which requires a source registration >>>> file. How do I get this file? Then once I have this file, will I be >>>> able to view step by step through the time series on the inflated volume? >>>> >>>> Thanks for your help, >>>> Anna >>>> >>>> >>>> === >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is currently ranked as the No. 2 hospital in the >>>> country by U.S. News & World Report (2017-2018). Visit us online at >>>> http://www.clevelandclinic.org for a complete listing of our services, >>>> staff and locations. Confidentiality Note: This message is intended >>>> for use only by the individual or entity to wh
Re: [Freesurfer] Re: Re: Re: Time Series to Surface
I just opened freeview and loaded everything in the GUI. I did not use the command line to open it. I do not see a slider bar. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu> Sent: Friday, April 6, 2018 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Re: Time Series to Surface what is your freeview command line? Do you see a "frame" slider bar? On 4/6/18 10:46 AM, Crawford, Anna wrote: > I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, > but I am still not able to view the time course. > > Thanks, > Anna > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve > <dgr...@mgh.harvard.edu> > Sent: Friday, April 6, 2018 10:21 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface > > No need to use --init-fsl (if using version 6). For mri_vol2surf add > --projfrac 0.5 to sample in the middle of the ribbon (unless you > specifically want to sample on the gray/white border) > > > On 4/6/18 10:11 AM, Crawford, Anna wrote: >> Hello, >> >> I used the following commands and then opened the surface as an overlay on >> the inflated volume, but I am not about to look at the time series. The view >> time course is grayed out so that I can not click on it. Did I miss a step >> or lose the actual time series somewhere? >> >> bbregister --s S2sdt/subject/ --mov >> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr >> --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5 >> >> mri_vol2surf --src >> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr >> --out >> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz >> --srcreg >> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat >> --hemi lh >> >> >> Thank you, >> Anna >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve >> <dgr...@mgh.harvard.edu> >> Sent: Thursday, April 5, 2018 5:29 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: [EXT] Re: [Freesurfer] Time Series to Surface >> >> Use bbregister. Run with --help to get docs (make sure to use --projfrac >> 0.5). Once you have it on the surface, you can step through each frame >> in freeview >> >> >> On 04/05/2018 01:49 PM, Crawford, Anna wrote: >>> Hello, >>> >>> I have a time series (.hdr/.img) that I want to overlay onto a >>> surface, specifically the inflated surface from the anatomy. I suspect >>> I have to use mri_vol2surf, which requires a source registration >>> file. How do I get this file? Then once I have this file, will I be >>> able to view step by step through the time series on the inflated volume? >>> >>> Thanks for your help, >>> Anna >>> >>> >>> === >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is currently ranked as the No. 2 hospital in the >>> country by U.S. News & World Report (2017-2018). Visit us online at >>> http://www.clevelandclinic.org for a complete listing of our services, >>> staff and locations. Confidentiality Note: This message is intended >>> for use only by the individual or entity to which it is addressed and >>> may contain information that is privileged, confidential, and exempt >>> from disclosure under applicable law. If the reader of this message is >>> not the intended recipient or the employee or agent responsible for >>> delivering the message to the intended recipient, you are hereby >>> notified that any dissemination, distribution or copying of this >>> communication is strictly prohibited. If you have received this >>> communication in error, please contact the sender immediately and >>> destroy the material in its entirety, whether electronic or hard copy. >>> Thank you. >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.
Re: [Freesurfer] Re: Re: Time Series to Surface
I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, but I am still not able to view the time course. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu> Sent: Friday, April 6, 2018 10:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Re: Time Series to Surface No need to use --init-fsl (if using version 6). For mri_vol2surf add --projfrac 0.5 to sample in the middle of the ribbon (unless you specifically want to sample on the gray/white border) On 4/6/18 10:11 AM, Crawford, Anna wrote: > Hello, > > I used the following commands and then opened the surface as an overlay on > the inflated volume, but I am not about to look at the time series. The view > time course is grayed out so that I can not click on it. Did I miss a step or > lose the actual time series somewhere? > > bbregister --s S2sdt/subject/ --mov > /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr > --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5 > > mri_vol2surf --src > /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr > --out > /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz > --srcreg > /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat > --hemi lh > > > Thank you, > Anna > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve > <dgr...@mgh.harvard.edu> > Sent: Thursday, April 5, 2018 5:29 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [EXT] Re: [Freesurfer] Time Series to Surface > > Use bbregister. Run with --help to get docs (make sure to use --projfrac > 0.5). Once you have it on the surface, you can step through each frame > in freeview > > > On 04/05/2018 01:49 PM, Crawford, Anna wrote: >> Hello, >> >> I have a time series (.hdr/.img) that I want to overlay onto a >> surface, specifically the inflated surface from the anatomy. I suspect >> I have to use mri_vol2surf, which requires a source registration >> file. How do I get this file? Then once I have this file, will I be >> able to view step by step through the time series on the inflated volume? >> >> Thanks for your help, >> Anna >> >> >> === >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is currently ranked as the No. 2 hospital in the >> country by U.S. News & World Report (2017-2018). Visit us online at >> http://www.clevelandclinic.org for a complete listing of our services, >> staff and locations. Confidentiality Note: This message is intended >> for use only by the individual or entity to which it is addressed and >> may contain information that is privileged, confidential, and exempt >> from disclosure under applicable law. If the reader of this message is >> not the intended recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are hereby >> notified that any dissemination, distribution or copying of this >> communication is strictly prohibited. If you have received this >> communication in error, please contact the sender immediately and >> destroy the material in its entirety, whether electronic or hard copy. >> Thank you. >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > === > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is currently ranked as the No. 2 hospital in the country by > U.S. News & World Report (2017-2018). Visit
Re: [Freesurfer] Re: Time Series to Surface
Hello, I used the following commands and then opened the surface as an overlay on the inflated volume, but I am not about to look at the time series. The view time course is grayed out so that I can not click on it. Did I miss a step or lose the actual time series somewhere? bbregister --s S2sdt/subject/ --mov /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5 mri_vol2surf --src /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr --out /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz --srcreg /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat --hemi lh Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Thursday, April 5, 2018 5:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re: [Freesurfer] Time Series to Surface Use bbregister. Run with --help to get docs (make sure to use --projfrac 0.5). Once you have it on the surface, you can step through each frame in freeview On 04/05/2018 01:49 PM, Crawford, Anna wrote: > Hello, > > I have a time series (.hdr/.img) that I want to overlay onto a > surface, specifically the inflated surface from the anatomy. I suspect > I have to use mri_vol2surf, which requires a source registration > file. How do I get this file? Then once I have this file, will I be > able to view step by step through the time series on the inflated volume? > > Thanks for your help, > Anna > > > === > > Please consider the environment before printing this e-mail > > Cleveland Clinic is currently ranked as the No. 2 hospital in the > country by U.S. News & World Report (2017-2018). Visit us online at > http://www.clevelandclinic.org for a complete listing of our services, > staff and locations. Confidentiality Note: This message is intended > for use only by the individual or entity to which it is addressed and > may contain information that is privileged, confidential, and exempt > from disclosure under applicable law. If the reader of this message is > not the intended recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are hereby > notified that any dissemination, distribution or copying of this > communication is strictly prohibited. If you have received this > communication in error, please contact the sender immediately and > destroy the material in its entirety, whether electronic or hard copy. > Thank you. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. === Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Time Series to Surface
Hello, I have a time series (.hdr/.img) that I want to overlay onto a surface, specifically the inflated surface from the anatomy. I suspect I have to use mri_vol2surf, which requires a source registration file. How do I get this file? Then once I have this file, will I be able to view step by step through the time series on the inflated volume? Thanks for your help, Anna === Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Hippocampal Sub-field volume units
Hello, i am using the hippocampal subfield segmentation. I am looking at the results in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was unsure of what the units were then in the .txt file. Does the .txt file give units in mm^3? * The sum of the number of voxels of a given structure multiplied by the volume of a voxel is not equal to the volume reported in [lr]h.hippoSfVolumes*.txt. This is because the volumes are computed upon a soft segmentation, rather than the discrete labels in [lr]h.hippoSfLabels*.mgz. This is the same that happens with the main recon-all stream: if you compute volumes by counting voxels in aseg.mgz, you don't get the values reported in aseg.stats. Thank you, Anna === Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Inflated Volume
Got it! Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Wednesday, March 1, 2017 11:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inflated Volume yea, you have to run it on a surface, usually the white, eg, mris_inflate -n 5 -no-save-sulc lh.white lh.inflated.anna On 03/01/2017 11:45 AM, Crawford, Anna wrote: > I did: > > mris_inflate -n 5 wmparc.mgz inflateTest.mgz > > I wasn't sure oh what my input file should be. It resulted in the following > message: > > No such file or directory > freadFloat: fread failed > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > Sent: Wednesday, March 1, 2017 11:41 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Inflated Volume > > what is your mris_inflate command line? > > > On 03/01/2017 11:20 AM, Crawford, Anna wrote: >> Hi, >> >> >> I am using a volume to create a surface overlay. I am currently >> overlaying onto the ?h.inflated volumes created when recon-all is >> executed. These volumes are overinflated for what I want. Is there a >> way I can create a less inflated, inflated-volume? I was looking at >> mris_inflate, and was thinking maybe it had to do with the iteration >> number. I was not able to get this command to execute though. Is there >> a way to do this? >> >> >> Thanks, >> >> Anna >> >> === >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by >> U.S.News & World Report (2015). Visit us online at >> http://www.clevelandclinic.org for a complete listing of our services, >> staff and locations. Confidentiality Note: This message is intended >> for use only by the individual or entity to which it is addressed and >> may contain information that is privileged, confidential, and exempt >> from disclosure under applicable law. If the reader of this message is >> not the intended recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are hereby >> notified that any dissemination, distribution or copying of this >> communication is strictly prohibited. If you have received this >> communication in error, please contact the sender immediately and >> destroy the material in its entirety, whether electronic or hard copy. >> Thank you. >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > === > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News > & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of > our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the > individual or entity to which it is addressed and may contain information > that is privileged, confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended recipient or the > employee or agent responsible for delivering the message to the in
Re: [Freesurfer] Inflated Volume
I did: mris_inflate -n 5 wmparc.mgz inflateTest.mgz I wasn't sure oh what my input file should be. It resulted in the following message: No such file or directory freadFloat: fread failed From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Wednesday, March 1, 2017 11:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inflated Volume what is your mris_inflate command line? On 03/01/2017 11:20 AM, Crawford, Anna wrote: > > Hi, > > > I am using a volume to create a surface overlay. I am currently > overlaying onto the ?h.inflated volumes created when recon-all is > executed. These volumes are overinflated for what I want. Is there a > way I can create a less inflated, inflated-volume? I was looking at > mris_inflate, and was thinking maybe it had to do with the iteration > number. I was not able to get this command to execute though. Is there > a way to do this? > > > Thanks, > > Anna > > === > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by > U.S.News & World Report (2015). Visit us online at > http://www.clevelandclinic.org for a complete listing of our services, > staff and locations. Confidentiality Note: This message is intended > for use only by the individual or entity to which it is addressed and > may contain information that is privileged, confidential, and exempt > from disclosure under applicable law. If the reader of this message is > not the intended recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are hereby > notified that any dissemination, distribution or copying of this > communication is strictly prohibited. If you have received this > communication in error, please contact the sender immediately and > destroy the material in its entirety, whether electronic or hard copy. > Thank you. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Inflated Volume
Hi, I am using a volume to create a surface overlay. I am currently overlaying onto the ?h.inflated volumes created when recon-all is executed. These volumes are overinflated for what I want. Is there a way I can create a less inflated, inflated-volume? I was looking at mris_inflate, and was thinking maybe it had to do with the iteration number. I was not able to get this command to execute though. Is there a way to do this? Thanks, Anna === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Remapping Volume
That seems to have worked and the regions are solid now. Thank you! Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, October 12, 2016 2:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Remapping Volume Try adding --projfrac 0.5 On 10/12/2016 11:29 AM, Crawford, Anna wrote: > I did: > > mri_vol2surf --src > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMnn.mgz > --out > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMnnS.mgh > --regheader segfs --hemi lh --surf white --out_type mgh --fixtkreg > > which resulted in the same type of surface. I looked at the volume and it > seemed as though things were labeled correctly. The images are attached. > > Thanks, > Anna > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, October 12, 2016 10:47 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Remapping Volume > > that seems ok, as I think the default is nearest neighbor. Can you > visualize the volume you created and see if the incorrect labels are in > it? > > On Wed, 12 Oct 2016, Crawford, Anna wrote: > >> I used: >> >> --src >> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMpostcent2.mgz >> --out >> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMpostcent2S.mgh >> --regheader segfs --hemi lh --surf white --out_type mgh >> >>> From the help file online, it looks like --fixtkreg would be used for the >>> nearest neighbor. What is the proper flag to set it to use nearest neighbor >>> interpolation? >> Thanks, >> Anna >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Tuesday, October 11, 2016 10:29 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Remapping Volume >> >> what was your vol2surf command line? Make sure that it is using nearest >> neighbor interpolation >> On Tue, 11 Oct 2016, Crawford, Anna wrote: >> >>> Hi, >>> >>> I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it >>> into Matlab using load_mgh. In Matlab I remap the volume to different >>> values. For example, all original values of 1022 will become 200 and all >>> 1030 values will become 150. (This is just an example, not necessarily these >>> numbers.) I save a new aparc+asegNew.mgz file using save_mgh. I use the same >>> M and mr_parms that I got when I loaded in the original file. I'm not sure >>> what these mean or if I need to change them. Then I use mri_vol2surf to >>> create a new surface overlay onto the inflated hemisphere. When I do this, >>> each region such as post central gyrus is 2 colors spotted together instead >>> of a solid color like in the original. I have attached pictures as an >>> example of what the original and remapped looked like. I didn't change the >>> location of values, just simple gave each value a new one. Why is the one >>> value speckled throughout? >>> >>> Thank you, >>> Anna >>> >>> === >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by >>> U.S.News & World Report (2015). Visit us online at >>> http://www.clevelandclinic.org for a complete listing of our services, staff >>> and locations. Confidentiality Note: This message is intended for use only >>> by the individual or entity to which it is addressed and may contain >>> information that is privileged, confidential, and exempt from disclosure >>> under applicable law. If the reader of this message is not the intended >>> recipient or the employee or agent responsible for delivering the message to >>> the intended recipient, you are hereby notified that any dissemination, >>> distribution or copying of this communication is strictly prohibited. If you >>> have received this communication in error, please contact the sender >>> immediately and destroy the material in its entirety, whether electronic or >>> hard copy.
Re: [Freesurfer] Remapping Volume
I used: --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMpostcent2.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegRMpostcent2S.mgh --regheader segfs --hemi lh --surf white --out_type mgh >From the help file online, it looks like --fixtkreg would be used for the >nearest neighbor. What is the proper flag to set it to use nearest neighbor >interpolation? Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Tuesday, October 11, 2016 10:29 PM To: Freesurfer support list Subject: Re: [Freesurfer] Remapping Volume what was your vol2surf command line? Make sure that it is using nearest neighbor interpolation On Tue, 11 Oct 2016, Crawford, Anna wrote: > Hi, > > I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it > into Matlab using load_mgh. In Matlab I remap the volume to different > values. For example, all original values of 1022 will become 200 and all > 1030 values will become 150. (This is just an example, not necessarily these > numbers.) I save a new aparc+asegNew.mgz file using save_mgh. I use the same > M and mr_parms that I got when I loaded in the original file. I'm not sure > what these mean or if I need to change them. Then I use mri_vol2surf to > create a new surface overlay onto the inflated hemisphere. When I do this, > each region such as post central gyrus is 2 colors spotted together instead > of a solid color like in the original. I have attached pictures as an > example of what the original and remapped looked like. I didn't change the > location of values, just simple gave each value a new one. Why is the one > value speckled throughout? > > Thank you, > Anna > > === > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by > U.S.News & World Report (2015). Visit us online at > http://www.clevelandclinic.org for a complete listing of our services, staff > and locations. Confidentiality Note: This message is intended for use only > by the individual or entity to which it is addressed and may contain > information that is privileged, confidential, and exempt from disclosure > under applicable law. If the reader of this message is not the intended > recipient or the employee or agent responsible for delivering the message to > the intended recipient, you are hereby notified that any dissemination, > distribution or copying of this communication is strictly prohibited. If you > have received this communication in error, please contact the sender > immediately and destroy the material in its entirety, whether electronic or > hard copy. Thank you. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Volume to Surface
When I do this for PET data for example and use the bbregister-generated.dat file, will that be with --srcreg bbregister-generated.dat ? If so, will I still use --regheader ? Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 1:17 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface yes, that's right. You will use mri_vol2surf with the identity matrix with the parcellation, but some bbregister-generated .dat file with PET data. cheers Bruce On Fri, 30 Sep 2016, Crawford, Anna wrote: > No problem. I'm not exactly sure, but I think I just want a surface overlay > so mri_vol2surf would be what I want. Right now, I am just trying to get > down the generic way of how to do it which is why I went with trying to > overlay the parcellation onto the inflated surface. Later, I will have > different modalities such as PET that I will want to overlay on the inflated > surface that will already be registered to the MRI. So I just wanted to get > the proper workflow of how to get a volume overlayed onto the surface if > that makes sense. > > Thank you, > Anna > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > Sent: Friday, September 30, 2016 10:48 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Volume to Surface > > Sorry - always helps to read the whole question :D > > So, you are trying to create an inflated white surface? As far as I know > this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and > inflated surfaces that are the pial pushed outwards. > > Also, "mri_vol2surf" creates surface overlays on surfaces that already > exist. > > Trisanna > > -- > Ph.D. Candidate McGill University > Integrated Program in Neuroscience > Psychology > > > On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org> wrote: > I already ran recall-all. I am trying to create a different > surface not created using recon-all. > > Anna > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna > Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] > Sent: Friday, September 30, 2016 10:40 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Volume to Surface > > You have to run recon-all to get the surfaces of a volume. > > Trisanna > > -- > Ph.D. Candidate McGill University > Integrated Program in Neuroscience > Psychology > > > On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org> > wrote: > Hello, > > I am trying to take nay volume that is registered and > create an inflated surface. I am trying to use > mri_vol2surf. I am having problems with the registration > source. From the examples I could fine, it should be > --srcreg *.dat. The only *.dat file I have is segment.dat > which does not work. I also tried using the white matter > volume which also didn't work. My input and output is > below. Could you offer some guidance on the registration > file? > > Thank you, > Anna > > mri_vol2surf --src > > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz > --out > > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh > --srcreg > > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat > --hemi lh --surf white --out_type paint > INFO: output format is paint > srcvol = > > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz > srcreg = > > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > regio_read_register(): Success > Error reading betplaneres from > > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat > > === > > Please consider th
Re: [Freesurfer] Volume to Surface
I'm not sure where to find the 140 220 220 0, but when I scrolled over what would seem to be the superior temporal area,I did have a value of 1030 which changed as I moved to different areas. I added the $h.aparc.annot annotations to confirm the locations and then compared to the .txt file for a few locations in the brain. The location numbers for my overlay matched the region of the brain. So, this seems as it worked properly. It is just a matter of color scheme not matching right? Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 4:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface examine the actual values. They should be constants that correspond to the values in $FREESURFER_HOME/FreeSurferColorLUT.txt, eg, left superior temporal gyrus should be 1030ctx-lh-superiortemporal 140 220 220 0 On 09/30/2016 04:15 PM, Crawford, Anna wrote: > I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a > similar type of surface to the one I had sent. > > mri_vol2surf --src > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz > --out > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh > --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5 > srcvol = > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz > srcreg unspecified > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > ProjFrac = 0.5 > thickness = thickness > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Computing registration from header. >Using > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as > target reference. > Reading surface > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white > Done reading source surface > Reading thickness > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness > Done > Mapping Source Volume onto Source Subject Surface > 1 0.5 0.5 0.5 > using old > Done mapping volume to surface > Number of source voxels hit = 73174 > Writing to > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh > Dim: 115984 1 1 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, September 30, 2016 3:52 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Volume to Surface > > You should use aparc+aseg.mgz and set the --projfrac 0.5. This should > produce something with the same information as the ?h.aparc.annot > (though the color scale will be different) > > > On 09/30/2016 03:51 PM, Crawford, Anna wrote: >> I was just using the wmparc as an example to get a volume overlay onto the >> surface. I chose that one just to see the parcellated surface similar to the >> volume. >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Friday, September 30, 2016 3:41 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Volume to Surface >> >> I can't tell from that image if it is right. Why are you mapping the >> wmparc to the surface? The wmparc will have segmentation boundaries >> right at the surface, so the actual value there will be unpredicatable. >> >> >> On 09/30/2016 03:31 PM, Crawford, Anna wrote: >>> Thank you everyone for your help! I do have a follow up question. I believe >>> this did what I wanted and is what I will want to do for PET data for >>> example. When I did the wmparc to the surface, I was expecting to see the >>> different areas mapped out similar to the volume. I have attached a screen >>> capture of what it looks like. Can someone confirm that this seems to be >>> correct and I was just expecting the wrong thing? I suspect this is the >>> case since to see the different areas in the volume you use the look up >>> table for the color map and that is not an option for the surface overlay. >>> >>> Thank you all again for your feedback! >>> >>> Anna >>> >>> From: frees
Re: [Freesurfer] Volume to Surface
I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a similar type of surface to the one I had sent. mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5 srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as target reference. Reading surface /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white Done reading source surface Reading thickness /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 73174 Writing to /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh Dim: 115984 1 1 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface You should use aparc+aseg.mgz and set the --projfrac 0.5. This should produce something with the same information as the ?h.aparc.annot (though the color scale will be different) On 09/30/2016 03:51 PM, Crawford, Anna wrote: > I was just using the wmparc as an example to get a volume overlay onto the > surface. I chose that one just to see the parcellated surface similar to the > volume. > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, September 30, 2016 3:41 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Volume to Surface > > I can't tell from that image if it is right. Why are you mapping the > wmparc to the surface? The wmparc will have segmentation boundaries > right at the surface, so the actual value there will be unpredicatable. > > > On 09/30/2016 03:31 PM, Crawford, Anna wrote: >> Thank you everyone for your help! I do have a follow up question. I believe >> this did what I wanted and is what I will want to do for PET data for >> example. When I did the wmparc to the surface, I was expecting to see the >> different areas mapped out similar to the volume. I have attached a screen >> capture of what it looks like. Can someone confirm that this seems to be >> correct and I was just expecting the wrong thing? I suspect this is the case >> since to see the different areas in the volume you use the look up table for >> the color map and that is not an option for the surface overlay. >> >> Thank you all again for your feedback! >> >> Anna >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Friday, September 30, 2016 2:42 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Volume to Surface >> >> Anna, try removing --out_type paint and instead specify the output file >> as wmparcSlh.mgh >> >> Trisanna, thanks so much for chipping in! >> >> >> >> On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote: >>> Ok so this is where my knowledge might be limited because you did a >>> slightly different thing than me by specifying the output type as >>> "paint" - that is what the .w format is. This is a label, I believe >>> and needs to be loaded as such. >>> >>> What happens if you try to remove the "output_type" and try to load >>> the result as an overlay? >>> >>> -- >>> Ph.D. Candidate >>> McGill University >>> Integrated Program in Neuroscience >>> Psychology >>> >>> >>> On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org >>> <mailto:crawf...@ccf.org>> wrote: >>> >>> Thank you! So good news, that worked and created wmparcSlh.w >>> >>> I'm not sure what the .w means. When I tr
Re: [Freesurfer] Volume to Surface
I was just using the wmparc as an example to get a volume overlay onto the surface. I chose that one just to see the parcellated surface similar to the volume. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface I can't tell from that image if it is right. Why are you mapping the wmparc to the surface? The wmparc will have segmentation boundaries right at the surface, so the actual value there will be unpredicatable. On 09/30/2016 03:31 PM, Crawford, Anna wrote: > Thank you everyone for your help! I do have a follow up question. I believe > this did what I wanted and is what I will want to do for PET data for > example. When I did the wmparc to the surface, I was expecting to see the > different areas mapped out similar to the volume. I have attached a screen > capture of what it looks like. Can someone confirm that this seems to be > correct and I was just expecting the wrong thing? I suspect this is the case > since to see the different areas in the volume you use the look up table for > the color map and that is not an option for the surface overlay. > > Thank you all again for your feedback! > > Anna > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, September 30, 2016 2:42 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Volume to Surface > > Anna, try removing --out_type paint and instead specify the output file > as wmparcSlh.mgh > > Trisanna, thanks so much for chipping in! > > > > On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote: >> Ok so this is where my knowledge might be limited because you did a >> slightly different thing than me by specifying the output type as >> "paint" - that is what the .w format is. This is a label, I believe >> and needs to be loaded as such. >> >> What happens if you try to remove the "output_type" and try to load >> the result as an overlay? >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org >> <mailto:crawf...@ccf.org>> wrote: >> >> Thank you! So good news, that worked and created wmparcSlh.w >> >> I'm not sure what the .w means. When I try to load it onto the >> surface, I get an error: "Failed to load Surface overlay." >> >> Thank you, >> Anna >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> [freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of >> Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca >> <mailto:trisanna.sprung-m...@mail.mcgill.ca>] >> *Sent:* Friday, September 30, 2016 12:51 PM >> >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] Volume to Surface >> >> My apologies, I meant "--regheader subject" >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org >> <mailto:crawf...@ccf.org>> wrote: >> >> Yeah, I get Error: Option unknown for --regmethod >> >> Anna >> >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> [freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of >> Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca >> <mailto:trisanna.sprung-m...@mail.mcgill.ca>] >> *Sent:* Friday, September 30, 2016 12:41 PM >> >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] Volume to Surface >> >> hmmm, yup not sure there. Did you try "--regmethod subject" >> >&g
Re: [Freesurfer] Volume to Surface
Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay." Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 12:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 12:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 11:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna Fr
Re: [Freesurfer] Volume to Surface
Yeah, I get Error: Option unknown for --regmethod Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 12:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 11:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org
Re: [Freesurfer] Volume to Surface
Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 11:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 201
Re: [Freesurfer] Volume to Surface
I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] Sent: Friday, September 30, 2016 11:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is inten
Re: [Freesurfer] Volume to Surface
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense. Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Sorry - always helps to read the whole question :D So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards. Also, "mri_vol2surf" creates surface overlays on surfaces that already exist. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance Help
Re: [Freesurfer] Volume to Surface
I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners C
[Freesurfer] Volume to Surface
Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Infalted/Label
i used dmax white. I now can see it on the inflated surface. Thank you for all your help in getting this working. Sorry, it took so long since I'm trying to figure all of this out still. The next step will be to take a volume that already has a selected region defined and projecting that region onto the inflated surface which I'm guessing will be somewhat similar to this. Thanks again, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 1:14 PM To: Douglas N Greve Cc: freesurfer@nmr.mgh.harvard.edu; Crawford, Anna; Anna Crawford Subject: Re: [Freesurfer] Infalted/Label you can also look at the vertex index of the first entry in the label file and type that into the "cursor" field in freeview so it will go to that point. My guess is that it does intersect the surface, otherwise the label indices would have stayed -1 On Thu, 29 Sep 2016, Douglas N Greve wrote: > Sounds like it. View the label on the volume while displaying the surfaces in > the volume and see if they intersect > > > On 09/29/2016 01:12 PM, Crawford, Anna wrote: >> I added the --paint option which seemed to run successfully. I loaded it as >> a label on the inflated surface and it did not crash, but I do not see it >> anywhere on the surface. Does this just mean that I didn't actually draw it >> on the surface? As in, everything was done correct, the location of the >> label isn't on the surface though. >> >> Thank you! >> Anna >> >> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] >> Sent: Thursday, September 29, 2016 12:45 PM >> To: Crawford, Anna; Bruce Fischl >> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu >> Subject: Re: Infalted/Label >> >> That is a volume-based label. Try using the --paint option to >> mri_label2label to convert it to a surface-based label (assuming it is >> actually on the surface). Run mri_label2label with --help to get an example >> >> >> On 09/29/2016 12:38 PM, Crawford, Anna wrote: >>> This is the output on label2label. The first colum of the created column >>> is -1. >>> >>> mri_label2label --srcsubject segfs --srclabel >>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label >>> --trgsubject segfs --trglabel Testing1N.label --regmethod volume >>> >>> srclabel = >>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label >>> srcsubject = segfs >>> trgsubject = segfs >>> trglabel = Testing1N.label >>> regmethod = volume >>> >>> usehash = 1 >>> Use ProjAbs = 0, 0 >>> Use ProjFrac = 0, 0 >>> DoPaint 0 >>> >>> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ >>> FREESURFER_HOME /tools/freesurfer >>> Loading source label. >>> Found 216 points in source label. >>> Starting volumetric mapping 216 points >>> Src2TrgVolReg: - >>>1.000 0.000 0.000 0.000; >>>0.000 1.000 0.000 -0.000; >>>0.000 -0.000 1.000 -0.000; >>>0.000 0.000 0.000 1.000; >>> 0 -39. 17. 55.-39. 17. 55. >>> 1 -38. 17. 55.-38. 17. 55. >>> 2 -40. 18. 55.-40. 18. 55. >>> 3 -39. 18. 55.-39. 18. 55. >>> 4 -38. 18. 55.-38. 18. 55. >>> Writing label file Testing1N.label 216 >>> mri_label2label: Done >>> >>> Thanks, >>> Anna >>> >>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >>> Sent: Thursday, September 29, 2016 12:29 PM >>> To: Crawford, Anna >>> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve >>> Subject: RE: Infalted/Label >>> >>> I'll cc the list, which I should have done the first time. No, you >>> didn't do anything wrong. This is what mri_label2label should do - sample >>> these locations onto the surface you specify and fill in the vertex >>> indices. Check the output of label2label and see if it has values >= 0 >>> cheers >>> Bruce >>> >>> On Thu, 29 Sep 2016, Crawford, Anna wrote: >>> >>>> Hi, >>>> >>>> I just checked all the labels I created and they all have -1 in the first >>>> col
Re: [Freesurfer] Infalted/Label
It seems as though I did something else wrong. I am guessing it has to do with dmax (I used inflated as my surface) for the --paint option. I had tried 0,1, and dmax as the input to the option. The new label it created only had 1 entry of all zeros which is why I cannot find it on the surface or the volume I would imagine. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 1:13 PM To: Crawford, Anna; Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu; Anna Crawford Subject: Re: [Freesurfer] Infalted/Label Sounds like it. View the label on the volume while displaying the surfaces in the volume and see if they intersect On 09/29/2016 01:12 PM, Crawford, Anna wrote: > I added the --paint option which seemed to run successfully. I loaded it as a > label on the inflated surface and it did not crash, but I do not see it > anywhere on the surface. Does this just mean that I didn't actually draw it > on the surface? As in, everything was done correct, the location of the label > isn't on the surface though. > > Thank you! > Anna > > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Thursday, September 29, 2016 12:45 PM > To: Crawford, Anna; Bruce Fischl > Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu > Subject: Re: Infalted/Label > > That is a volume-based label. Try using the --paint option to > mri_label2label to convert it to a surface-based label (assuming it is > actually on the surface). Run mri_label2label with --help to get an example > > > On 09/29/2016 12:38 PM, Crawford, Anna wrote: >> This is the output on label2label. The first colum of the created column is >> -1. >> >> mri_label2label --srcsubject segfs --srclabel >> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label >> --trgsubject segfs --trglabel Testing1N.label --regmethod volume >> >> srclabel = >> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label >> srcsubject = segfs >> trgsubject = segfs >> trglabel = Testing1N.label >> regmethod = volume >> >> usehash = 1 >> Use ProjAbs = 0, 0 >> Use ProjFrac = 0, 0 >> DoPaint 0 >> >> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ >> FREESURFER_HOME /tools/freesurfer >> Loading source label. >> Found 216 points in source label. >> Starting volumetric mapping 216 points >> Src2TrgVolReg: - >>1.000 0.000 0.000 0.000; >>0.000 1.000 0.000 -0.000; >>0.000 -0.000 1.000 -0.000; >>0.000 0.000 0.000 1.000; >> 0 -39. 17. 55.-39. 17. 55. >> 1 -38. 17. 55.-38. 17. 55. >> 2 -40. 18. 55.-40. 18. 55. >> 3 -39. 18. 55.-39. 18. 55. >> 4 -38. 18. 55.-38.0000 18. 55. >> Writing label file Testing1N.label 216 >> mri_label2label: Done >> >> Thanks, >> Anna >> >> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >> Sent: Thursday, September 29, 2016 12:29 PM >> To: Crawford, Anna >> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve >> Subject: RE: Infalted/Label >> >> I'll cc the list, which I should have done the first time. No, you >> didn't do anything wrong. This is what mri_label2label should do - sample >> these locations onto the surface you specify and fill in the vertex >> indices. Check the output of label2label and see if it has values >= 0 >> cheers >> Bruce >> >> On Thu, 29 Sep 2016, Crawford, Anna wrote: >> >>> Hi, >>> >>> I just checked all the labels I created and they all have -1 in the first >>> column (the file name ending in 'N' should be the one created from >>> mri_label2label). So, I did something wrong when originally creating the >>> label I assume. When I created it, under the ROI tab, I created a new one >>> and then drew it in the viewer with a volume (I did both white matter and >>> brain mask) also loaded. Was this wrong? >>> >>> Thank you, >>> Anna >>> >>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >>> Sent: Thursday, September 29, 2016 12:00 PM >>> To: Crawford, Anna >>> Cc: Anna Crawford; Douglas N.
Re: [Freesurfer] Infalted/Label
I added the --paint option which seemed to run successfully. I loaded it as a label on the inflated surface and it did not crash, but I do not see it anywhere on the surface. Does this just mean that I didn't actually draw it on the surface? As in, everything was done correct, the location of the label isn't on the surface though. Thank you! Anna From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:45 PM To: Crawford, Anna; Bruce Fischl Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu Subject: Re: Infalted/Label That is a volume-based label. Try using the --paint option to mri_label2label to convert it to a surface-based label (assuming it is actually on the surface). Run mri_label2label with --help to get an example On 09/29/2016 12:38 PM, Crawford, Anna wrote: > This is the output on label2label. The first colum of the created column is > -1. > > mri_label2label --srcsubject segfs --srclabel > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label > --trgsubject segfs --trglabel Testing1N.label --regmethod volume > > srclabel = > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label > srcsubject = segfs > trgsubject = segfs > trglabel = Testing1N.label > regmethod = volume > > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ > FREESURFER_HOME /tools/freesurfer > Loading source label. > Found 216 points in source label. > Starting volumetric mapping 216 points > Src2TrgVolReg: - > 1.000 0.000 0.000 0.000; > 0.000 1.000 0.000 -0.000; > 0.000 -0.000 1.000 -0.000; > 0.000 0.000 0.000 1.000; >0 -39. 17. 55.-39. 17. 55. >1 -38. 17. 55.-38. 17. 55. >2 -40. 18. 55.-40. 18. 55. >3 -39. 18. 55.-39. 18. 55. >4 -38. 18. 55.-38. 18. 55. > Writing label file Testing1N.label 216 > mri_label2label: Done > > Thanks, > Anna > ________ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, September 29, 2016 12:29 PM > To: Crawford, Anna > Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve > Subject: RE: Infalted/Label > > I'll cc the list, which I should have done the first time. No, you > didn't do anything wrong. This is what mri_label2label should do - sample > these locations onto the surface you specify and fill in the vertex > indices. Check the output of label2label and see if it has values >= 0 > cheers > Bruce > > On Thu, 29 Sep 2016, Crawford, Anna wrote: > >> Hi, >> >> I just checked all the labels I created and they all have -1 in the first >> column (the file name ending in 'N' should be the one created from >> mri_label2label). So, I did something wrong when originally creating the >> label I assume. When I created it, under the ROI tab, I created a new one >> and then drew it in the viewer with a volume (I did both white matter and >> brain mask) also loaded. Was this wrong? >> >> Thank you, >> Anna >> >> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >> Sent: Thursday, September 29, 2016 12:00 PM >> To: Crawford, Anna >> Cc: Anna Crawford; Douglas N. Greve >> Subject: RE: Infalted/Label >> >> Hi Anna >> >> the label you send me hasn't been sampled onto the surface, which is why >> it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You >> can tell this is the case as the first column has all -1. If it had been >> sampled onto the surface these values would be in [0, nvertices]. >> >> Does you newer one have non-zero values in this column? >> >> cheers >> Bruce >> >> On Thu, 29 Sep 2016, >> Crawford, Anna wrote: >> >>> It is in the left hemisphere. >>> >>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >>> Sent: Thursday, September 29, 2016 10:38 AM >>> To: Anna Crawford >>> Cc: Crawford, Anna; Douglas N. Greve >>> Subject: Re: Infalted/Label >>> >>> are the labels lh or rh? >>> On Wed, 28 Sep 2016, Anna Crawford wrote: >>> >>>> Hopefully this works better for you. Thank you, >>>> >>>> Anna >>>> >>>> >>> >>> The information in this e-mail is intended only for the perso
Re: [Freesurfer] Infalted/Label
This is the output on label2label. The first colum of the created column is -1. mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: - 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39. 17. 55.-39. 17. 55. 1 -38. 17. 55.-38. 17. 55. 2 -40. 18. 55.-40. 18. 55. 3 -39. 18. 55.-39. 18. 55. 4 -38. 18. 55.-38. 18. 55. Writing label file Testing1N.label 216 mri_label2label: Done Thanks, Anna From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, September 29, 2016 12:29 PM To: Crawford, Anna Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve Subject: RE: Infalted/Label I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce On Thu, 29 Sep 2016, Crawford, Anna wrote: > Hi, > > I just checked all the labels I created and they all have -1 in the first > column (the file name ending in 'N' should be the one created from > mri_label2label). So, I did something wrong when originally creating the > label I assume. When I created it, under the ROI tab, I created a new one and > then drew it in the viewer with a volume (I did both white matter and brain > mask) also loaded. Was this wrong? > > Thank you, > Anna > > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, September 29, 2016 12:00 PM > To: Crawford, Anna > Cc: Anna Crawford; Douglas N. Greve > Subject: RE: Infalted/Label > > Hi Anna > > the label you send me hasn't been sampled onto the surface, which is why > it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You > can tell this is the case as the first column has all -1. If it had been > sampled onto the surface these values would be in [0, nvertices]. > > Does you newer one have non-zero values in this column? > > cheers > Bruce > > On Thu, 29 Sep 2016, > Crawford, Anna wrote: > >> It is in the left hemisphere. >> >> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >> Sent: Thursday, September 29, 2016 10:38 AM >> To: Anna Crawford >> Cc: Crawford, Anna; Douglas N. Greve >> Subject: Re: Infalted/Label >> >> are the labels lh or rh? >> On Wed, 28 Sep 2016, Anna Crawford wrote: >> >>> Hopefully this works better for you. Thank you, >>> >>> Anna >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> === >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by >> U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of >> our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the >> individual or entity to which it is addressed and may contain information >> that is privileged, confidential, and exempt from disclosure under >> applicable law. If the reader of this message is not the intended recipient >> or the employee or agent responsible for delivering the message to the >> intended recipient, you are hereby notified that any
Re: [Freesurfer] Co-registering different source data
I get a different error when I use --regmethod surface (below). I double checked that I am in the correct hemishpere. I'm not sure if it has to do with teh volume I used to draw to ROI or something with how I drew it. Thanks, Anna mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1Ns.label --regmethod surface --hemi lh srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1Ns.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting surface-based mapping Reading source registration /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white Reading target registration /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created. Label point 0: vno = -1, max = 115984 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 5:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data Is Testing1.label a surface-based label? If so, use --regmethod surface On 09/28/2016 04:39 PM, Crawford, Anna wrote: > The subject path was > /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, September 28, 2016 4:35 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > which lh.inflated and rh.inflated did you load? That is, for which > subject? > On Wed, 28 Sep 2016, Crawford, Anna wrote: > >> I just opened freeview (just typed freeview into the command line). Then >> from inside freeview, under the surfaces tab, I loaded the lh.inflated and >> rh.inflated. Also under the surfaces tab, under Label I chose the label file >> created (Testing1N.label). When I tried to open the label, is when Freeview >> crashed. >> >> Thanks, >> >> Anna >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, September 28, 2016 4:27 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> what was your freeview command line, and what did you do to make it crash? >> >> On Wed, 28 Sep 2016, Crawford, Anna wrote: >> >>> Thank you! that seemed to have worked. I thought I had tried that before, >>> but must not that. The input/output is below. The new label was created. >>> When I tried to load the label onto the surface, FreeView crashed the same >>> as it did before though which brings me back to my original problem on >>> Freeview crashing when I try to put the label on the surface. Do I need to >>> change the label to a volume/surface to get this to work? >>> >>> Thanks, >>> >>> Anna >>> >>> mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject >>> segfs --trglabel Testing1N.label --regmethod volume >>> >>> srclabel = Testing1.label >>> srcsubject = segfs >>> trgsubject = segfs >>> trglabel = Testing1N.label >>> regmethod = volume >>> >>> usehash = 1 >>> Use ProjAbs = 0, 0 >>> Use ProjFrac = 0, 0 >>> DoPaint 0 >>> >>> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ >>> FREESURFER_HOME /tools/freesurfer >>> Loading source label. >>> No such file or directory >>&g
Re: [Freesurfer] Co-registering different source data
The subject path was /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data which lh.inflated and rh.inflated did you load? That is, for which subject? On Wed, 28 Sep 2016, Crawford, Anna wrote: > I just opened freeview (just typed freeview into the command line). Then from > inside freeview, under the surfaces tab, I loaded the lh.inflated and > rh.inflated. Also under the surfaces tab, under Label I chose the label file > created (Testing1N.label). When I tried to open the label, is when Freeview > crashed. > > Thanks, > > Anna > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, September 28, 2016 4:27 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > what was your freeview command line, and what did you do to make it crash? > > On Wed, 28 Sep 2016, Crawford, Anna wrote: > >> Thank you! that seemed to have worked. I thought I had tried that before, >> but must not that. The input/output is below. The new label was created. >> When I tried to load the label onto the surface, FreeView crashed the same >> as it did before though which brings me back to my original problem on >> Freeview crashing when I try to put the label on the surface. Do I need to >> change the label to a volume/surface to get this to work? >> >> Thanks, >> >> Anna >> >> mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject >> segfs --trglabel Testing1N.label --regmethod volume >> >> srclabel = Testing1.label >> srcsubject = segfs >> trgsubject = segfs >> trglabel = Testing1N.label >> regmethod = volume >> >> usehash = 1 >> Use ProjAbs = 0, 0 >> Use ProjFrac = 0, 0 >> DoPaint 0 >> >> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ >> FREESURFER_HOME /tools/freesurfer >> Loading source label. >> No such file or directory >> mri_label2label: could not open label file Testing1.label >> No such file or directory >> ERROR reading Testing1.label >> [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel >> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label >> --trgsubject segfs --trglabel Testing1N.label --regmethod volume >> >> srclabel = >> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label >> srcsubject = segfs >> trgsubject = segfs >> trglabel = Testing1N.label >> regmethod = volume >> >> usehash = 1 >> Use ProjAbs = 0, 0 >> Use ProjFrac = 0, 0 >> DoPaint 0 >> >> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ >> FREESURFER_HOME /tools/freesurfer >> Loading source label. >> Found 216 points in source label. >> Starting volumetric mapping 216 points >> Src2TrgVolReg: - >> 1.000 0.000 0.000 0.000; >> 0.000 1.000 0.000 -0.000; >> 0.000 -0.000 1.000 -0.000; >> 0.000 0.000 0.000 1.000; >> 0 -39. 17. 55.-39. 17. 55. >> 1 -38. 17. 55.-38. 17. 55. >> 2 -40. 18. 55.-40. 18. 55. >> 3 -39. 18. 55.-39. 18. 55. >> 4 -38. 18. 55.-38. 18. 55. >> Writing label file Testing1N.label 216 >> mri_label2label: Done >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Wednesday, September 28, 2016 4:08 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Try giving it the full path to the label, ie, >> >> --srclabel >> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label >> >> On 9/28/16 3:47 PM, Crawford, Anna wrote: >>> Hi, >>> >>> Below is the command I entered with the output containing the error. I also >>> tried different variations on the path for the directory, but this is the >
Re: [Freesurfer] Co-registering different source data
I just opened freeview (just typed freeview into the command line). Then from inside freeview, under the surfaces tab, I loaded the lh.inflated and rh.inflated. Also under the surfaces tab, under Label I chose the label file created (Testing1N.label). When I tried to open the label, is when Freeview crashed. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data what was your freeview command line, and what did you do to make it crash? On Wed, 28 Sep 2016, Crawford, Anna wrote: > Thank you! that seemed to have worked. I thought I had tried that before, but > must not that. The input/output is below. The new label was created. When I > tried to load the label onto the surface, FreeView crashed the same as it did > before though which brings me back to my original problem on Freeview > crashing when I try to put the label on the surface. Do I need to change the > label to a volume/surface to get this to work? > > Thanks, > > Anna > > mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject > segfs --trglabel Testing1N.label --regmethod volume > > srclabel = Testing1.label > srcsubject = segfs > trgsubject = segfs > trglabel = Testing1N.label > regmethod = volume > > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ > FREESURFER_HOME /tools/freesurfer > Loading source label. > No such file or directory > mri_label2label: could not open label file Testing1.label > No such file or directory > ERROR reading Testing1.label > [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label > --trgsubject segfs --trglabel Testing1N.label --regmethod volume > > srclabel = > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label > srcsubject = segfs > trgsubject = segfs > trglabel = Testing1N.label > regmethod = volume > > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ > FREESURFER_HOME /tools/freesurfer > Loading source label. > Found 216 points in source label. > Starting volumetric mapping 216 points > Src2TrgVolReg: - > 1.000 0.000 0.000 0.000; > 0.000 1.000 0.000 -0.000; > 0.000 -0.000 1.000 -0.000; > 0.000 0.000 0.000 1.000; > 0 -39. 17. 55.-39. 17. 55. > 1 -38. 17. 55.-38. 17. 55. > 2 -40. 18. 55.-40. 18. 55. > 3 -39. 18. 55.-39. 18. 55. > 4 -38. 18. 55.-38. 18. 55. > Writing label file Testing1N.label 216 > mri_label2label: Done > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, September 28, 2016 4:08 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Co-registering different source data > > Try giving it the full path to the label, ie, > > --srclabel > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label > > On 9/28/16 3:47 PM, Crawford, Anna wrote: >> Hi, >> >> Below is the command I entered with the output containing the error. I also >> tried different variations on the path for the directory, but this is the >> one I thought it should be. >> >> Thanks, >> Anna >> >> mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject >> segfs --trglabel Testing1N.label --regmethod volume >> >> srclabel = Testing1.label >> srcsubject = segfs >> trgsubject = segfs >> trglabel = Testing1N.label >> regmethod = volume >> >> usehash = 1 >> Use ProjAbs = 0, 0 >> Use ProjFrac = 0, 0 >> DoPaint 0 >> >> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ >> FREESURFER_HOME /tools/freesurfer >> Loading source label. >> No such file or directory >> mri_label2label: could not open label file Testing1.label >> No such file or directory >> ERROR reading Testing1.label >> __ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-bou
Re: [Freesurfer] Co-registering different source data
Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on Freeview crashing when I try to put the label on the surface. Do I need to change the label to a volume/surface to get this to work? Thanks, Anna mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: - 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39. 17. 55.-39. 17. 55. 1 -38. 17. 55.-38. 17. 55. 2 -40. 18. 55.-40. 18. 55. 3 -39. 18. 55.-39. 18. 55. 4 -38. 18. 55.-38. 18. 55. Writing label file Testing1N.label 216 mri_label2label: Done From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data Try giving it the full path to the label, ie, --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label On 9/28/16 3:47 PM, Crawford, Anna wrote: > Hi, > > Below is the command I entered with the output containing the error. I also > tried different variations on the path for the directory, but this is the one > I thought it should be. > > Thanks, > Anna > > mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject > segfs --trglabel Testing1N.label --regmethod volume > > srclabel = Testing1.label > srcsubject = segfs > trgsubject = segfs > trglabel = Testing1N.label > regmethod = volume > > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ > FREESURFER_HOME /tools/freesurfer > Loading source label. > No such file or directory > mri_label2label: could not open label file Testing1.label > No such file or directory > ERROR reading Testing1.label > __ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, September 28, 2016 3:11 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > sorry, I've lost track of where this is at. Can you send us the full > screen output of the command you tried to run and the error it gives? > > thanks > Bruce > On > Tue, 27 Sep 2016, Crawford, Anna wrote: > >> I have tried multiple variations for my subject directory. I have had it end >> at study11074, S2sdt, segfs, and label. I suspected it should either be >> S2sdt or segfs. I get the same error in all cases still. When using a >> differnt function with the subject directory path, I had ended at S2sdt, the >> subject was segfs, and then the file I wanted to use. I thought it would be >> the same in the case in that regard, but it doesn't seem to be working that >> way. >> >> Thank you, >> Anna >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw >> [dgwake...@gmail.com] >> Sent
Re: [Freesurfer] Co-registering different source data
Hi,
Below is the command I entered with the output containing the error. I also
tried different variations on the path for the directory, but this is the one I
thought it should be.
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs
--trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label
srcsubject = segfs
trgsubject = segfs
trglabel = Testing1N.label
regmethod = volume
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
FREESURFER_HOME /tools/freesurfer
Loading source label.
No such file or directory
mri_label2label: could not open label file Testing1.label
No such file or directory
ERROR reading Testing1.label
__
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, September 28, 2016 3:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full
screen output of the command you tried to run and the error it gives?
thanks
Bruce
On
Tue, 27 Sep 2016, Crawford, Anna wrote:
> I have tried multiple variations for my subject directory. I have had it end
> at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt
> or segfs. I get the same error in all cases still. When using a differnt
> function with the subject directory path, I had ended at S2sdt, the subject
> was segfs, and then the file I wanted to use. I thought it would be the same
> in the case in that regard, but it doesn't seem to be working that way.
>
> Thank you,
> Anna
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw
> [dgwake...@gmail.com]
> Sent: Tuesday, September 27, 2016 12:04 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> I think you SUBJECTS_DIR might be set incorrectly,
>
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
>
> I suspect the value should be:
>
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
>
> or possibly something else:
>
> ${SUBJECTS_DIR}/$SUBJECT/label/
> should be the directory with Testing.label
>
> hth
> d
>
> On 9/27/16 11:58 AM, Crawford, Anna wrote:
>> Th output is below:
>>
>> aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label
>>rh.BA4p.label
>> aparc.annot.ctab lh.BA45.thresh.label
>> rh.aparc.a2009s.annot rh.BA4p.thresh.label
>> aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot
>>rh.BA6.label
>> BA.ctab lh.BA4a.thresh.label
>> rh.aparc.DKTatlas40.annot rh.BA6.thresh.label
>> BA.thresh.ctab lh.BA4p.label rh.BA1.label
>>rh.BA.annot
>> lh.aparc.a2009s.annotlh.BA4p.thresh.labelrh.BA1.thresh.label
>>rh.BA.thresh.annot
>> lh.aparc.annot lh.BA6.labelrh.BA2.label
>>rh.cortex.label
>> lh.aparc.DKTatlas40.annotlh.BA6.thresh.label rh.BA2.thresh.label
>>rh.entorhinal_exvivo.label
>> lh.BA1.label lh.BA.annot rh.BA3a.label
>>rh.MT.label
>> lh.BA1.thresh.label lh.BA.thresh.annot
>> rh.BA3a.thresh.label rh.MT.thresh.label
>> lh.BA2.label lh.cortex.label rh.BA3b.label
>>rh.perirhinal.label
>> lh.BA2.thresh.label lh.entorhinal_exvivo.label
>> rh.BA3b.thresh.label rh.V1.label
>> lh.BA3a.labellh.MT.label rh.BA44.label
>>rh.V1.thresh.label
>> lh.BA3a.thresh.label lh.MT.thresh.label
>> rh.BA44.thresh.label rh.V2.label
>> lh.BA3b.labellh.perirhinal.label rh.BA45.label
>>rh.V2.thresh.label
>> lh.BA3b.thresh.label lh.V1.label
>> rh.BA45.thresh.label Testing1.label
>> lh.BA44.labellh.V1.thresh.label rh.BA4a.label
>>Testing.label
>> lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
>>
>> Thanks,
>> Anna
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw
>> [dgwake...@gma
Re: [Freesurfer] Co-registering different source data
I have tried multiple variations for my subject directory. I have had it end at
study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or
segfs. I get the same error in all cases still. When using a differnt function
with the subject directory path, I had ended at S2sdt, the subject was segfs,
and then the file I wanted to use. I thought it would be the same in the case
in that regard, but it doesn't seem to be working that way.
Thank you,
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw [dgwake...@gmail.com]
Sent: Tuesday, September 27, 2016 12:04 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/
should be the directory with Testing.label
hth
d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
> Th output is below:
>
> aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label
> rh.BA4p.label
> aparc.annot.ctab lh.BA45.thresh.label
> rh.aparc.a2009s.annot rh.BA4p.thresh.label
> aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot
> rh.BA6.label
> BA.ctab lh.BA4a.thresh.label
> rh.aparc.DKTatlas40.annot rh.BA6.thresh.label
> BA.thresh.ctab lh.BA4p.label rh.BA1.label
> rh.BA.annot
> lh.aparc.a2009s.annotlh.BA4p.thresh.labelrh.BA1.thresh.label
> rh.BA.thresh.annot
> lh.aparc.annot lh.BA6.labelrh.BA2.label
> rh.cortex.label
> lh.aparc.DKTatlas40.annotlh.BA6.thresh.label rh.BA2.thresh.label
> rh.entorhinal_exvivo.label
> lh.BA1.label lh.BA.annot rh.BA3a.label
> rh.MT.label
> lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label
> rh.MT.thresh.label
> lh.BA2.label lh.cortex.label rh.BA3b.label
> rh.perirhinal.label
> lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label
> rh.V1.label
> lh.BA3a.labellh.MT.label rh.BA44.label
> rh.V1.thresh.label
> lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label
> rh.V2.label
> lh.BA3b.labellh.perirhinal.label rh.BA45.label
> rh.V2.thresh.label
> lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label
> Testing1.label
> lh.BA44.labellh.V1.thresh.label rh.BA4a.label
> Testing.label
> lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
>
> Thanks,
> Anna
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw
> [dgwake...@gmail.com]
> Sent: Tuesday, September 27, 2016 11:52 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> what is the output of "ls"?
>
>
> On 9/27/16 11:50 AM, Crawford, Anna wrote:
>> Thank you. That worked for changing the default directory. When I run
>> mri_label2label, I am still getting the same error that there is no such
>> file or directory for the label.
>>
>> Anna
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw
>> [dgwake...@gmail.com]
>> Sent: Tuesday, September 27, 2016 11:36 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Co-registering different source data
>>
>> Anna, if you are using bash the command is:
>>
>> export SUBJECTS_DIR=
>>
>>
>> On 9/27/16 11:31 AM, Crawford, Anna wrote:
>>> I also tried doing setenv SUBJECTS_DIR but that did not work either.
>>>
>>> bash: setenv: command not found
>>>
>>> Thanks,
>>> Anna
>>>
>>> From: Crawford, Anna
>>> Sent: Tuesday, September 27, 2016 11:12 AM
>>> To: Freesurfer support list
>>> Subject: RE: [Freesurfer] Co-registering different source data
>>>
>>> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR
>>> /tools/freesurfer/subjects) which is n
Re: [Freesurfer] Co-registering different source data
Th output is below: aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.labelrh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annotlh.BA4p.thresh.labelrh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.labelrh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annotlh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.labellh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.labellh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.labellh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw [dgwake...@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data what is the output of "ls"? On 9/27/16 11:50 AM, Crawford, Anna wrote: > Thank you. That worked for changing the default directory. When I run > mri_label2label, I am still getting the same error that there is no such file > or directory for the label. > > Anna > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw > [dgwake...@gmail.com] > Sent: Tuesday, September 27, 2016 11:36 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Anna, if you are using bash the command is: > > export SUBJECTS_DIR= > > > On 9/27/16 11:31 AM, Crawford, Anna wrote: >> I also tried doing setenv SUBJECTS_DIR but that did not work either. >> >> bash: setenv: command not found >> >> Thanks, >> Anna >> >> From: Crawford, Anna >> Sent: Tuesday, September 27, 2016 11:12 AM >> To: Freesurfer support list >> Subject: RE: [Freesurfer] Co-registering different source data >> >> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR >> /tools/freesurfer/subjects) which is not where my data is located. >> >> Thanks, >> Anna >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Tuesday, September 27, 2016 10:50 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that >> is already set properly, then do not use the --sd. >> >> >> On 9/27/16 9:38 AM, Crawford, Anna wrote: >>> Hi, >>> >>> I keep getting an error when I use mri_label2label. Below is my input and >>> output. I have tried various paths all the way down to the label and above >>> the subject level, but still always get the same error. I have also >>> verified it is the path with the label. Why is it not recognizing it? >>> >>> Thank you, >>> Anna >>> >>> >>> mri_label2label --sd >>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label >>> --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel >>> Testing1N.label --regmethod volume >>> >>> srclabel = Testing.label >>> srcsubject = segfs >>> trgsubject = segfs >>> trglabel = Test
Re: [Freesurfer] Co-registering different source data
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label. Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw [dgwake...@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data Anna, if you are using bash the command is: export SUBJECTS_DIR= On 9/27/16 11:31 AM, Crawford, Anna wrote: > I also tried doing setenv SUBJECTS_DIR but that did not work either. > > bash: setenv: command not found > > Thanks, > Anna > ____ > From: Crawford, Anna > Sent: Tuesday, September 27, 2016 11:12 AM > To: Freesurfer support list > Subject: RE: [Freesurfer] Co-registering different source data > > If I don't use --sd it uses the default subject directory (SUBJECTS_DIR > /tools/freesurfer/subjects) which is not where my data is located. > > Thanks, > Anna > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, September 27, 2016 10:50 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Co-registering different source data > > Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that > is already set properly, then do not use the --sd. > > > On 9/27/16 9:38 AM, Crawford, Anna wrote: >> Hi, >> >> I keep getting an error when I use mri_label2label. Below is my input and >> output. I have tried various paths all the way down to the label and above >> the subject level, but still always get the same error. I have also verified >> it is the path with the label. Why is it not recognizing it? >> >> Thank you, >> Anna >> >> >> mri_label2label --sd >> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label >> --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel >> Testing1N.label --regmethod volume >> >> srclabel = Testing.label >> srcsubject = segfs >> trgsubject = segfs >> trglabel = Testing1N.label >> regmethod = volume >> >> usehash = 1 >> Use ProjAbs = 0, 0 >> Use ProjFrac = 0, 0 >> DoPaint 0 >> >> SUBJECTS_DIR >> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label >> FREESURFER_HOME /tools/freesurfer >> Loading source label. >> No such file or directory >> mri_label2label: could not open label file Testing.label >> No such file or directory >> ERROR reading Testing.label >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 6:20 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Hi Anna >> >> freeview now checks (in the dev version I believe) if the label has been >> sampled onto the surface and won't crash, but you need to use >> mri_label2label to sample it onto the surface before loading it onto the >> inflated surface in freeview >> >> cheers >> Bruce >> >> >> On Mon, 26 Sep 2016, Crawford, Anna wrote: >> >>> Hi, >>> >>> i created a test ROI which saves as a label. Every time I try to load it as >>> a label on the surface (inflated), it crashed FreeView. I'm not sure why it >>> won't load there. I noticed this happens with some other ore-made labels as >>> well. What could be the cause of this? >>> >>> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an >>> errorL option unknown. I did the following: >>> >>> mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz >>> >>> among other similar variations. Am I just inputting it wrong or am I just >>> missing information? >>> >>> Thank you, >>> Anna >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 4:23 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >
Re: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd. On 9/27/16 9:38 AM, Crawford, Anna wrote: > Hi, > > I keep getting an error when I use mri_label2label. Below is my input and > output. I have tried various paths all the way down to the label and above > the subject level, but still always get the same error. I have also verified > it is the path with the label. Why is it not recognizing it? > > Thank you, > Anna > > > mri_label2label --sd > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label > --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel > Testing1N.label --regmethod volume > > srclabel = Testing.label > srcsubject = segfs > trgsubject = segfs > trglabel = Testing1N.label > regmethod = volume > > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR > /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label > FREESURFER_HOME /tools/freesurfer > Loading source label. > No such file or directory > mri_label2label: could not open label file Testing.label > No such file or directory > ERROR reading Testing.label > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 6:20 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > freeview now checks (in the dev version I believe) if the label has been > sampled onto the surface and won't crash, but you need to use > mri_label2label to sample it onto the surface before loading it onto the > inflated surface in freeview > > cheers > Bruce > > > On Mon, 26 Sep 2016, Crawford, Anna wrote: > >> Hi, >> >> i created a test ROI which saves as a label. Every time I try to load it as >> a label on the surface (inflated), it crashed FreeView. I'm not sure why it >> won't load there. I noticed this happens with some other ore-made labels as >> well. What could be the cause of this? >> >> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an >> errorL option unknown. I did the following: >> >> mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz >> >> among other similar variations. Am I just inputting it wrong or am I just >> missing information? >> >> Thank you, >> Anna >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 4:23 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Hi Anna >> >> scuba is very old and deprecated. Try using freeview instead >> >> cheers >> Bruce >> On Mon, 26 Sep >> 2016, Crawford, Anna wrote: >> >>> To create the volume ROI, I found something that said to use: >>> >>> scuba -v $filename >>> >>> to then make a new ROI. >>> >>> I got en error that I could not open scuba. Is this the correct way to go >>> about this, or is there some other means that I should be doing not 'scuba'? >>> >>> Thank you, >>> Anna >>> ________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 1:52 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> yes, create a volume ROI and you can map it onto the surface using >>> mri_vol2surf >>> >>> cheers >>> Bruce >>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>> >>>> For now, I am just trying to
Re: [Freesurfer] Co-registering different source data
Hi, I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it? Thank you, Anna mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data Hi Anna freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote: > Hi, > > i created a test ROI which saves as a label. Every time I try to load it as a > label on the surface (inflated), it crashed FreeView. I'm not sure why it > won't load there. I noticed this happens with some other ore-made labels as > well. What could be the cause of this? > > I also tried doing mri_label2vol (to then do vol2surf), but I am getting an > errorL option unknown. I did the following: > > mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz > > among other similar variations. Am I just inputting it wrong or am I just > missing information? > > Thank you, > Anna > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 4:23 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > scuba is very old and deprecated. Try using freeview instead > > cheers > Bruce > On Mon, 26 Sep > 2016, Crawford, Anna wrote: > >> To create the volume ROI, I found something that said to use: >> >> scuba -v $filename >> >> to then make a new ROI. >> >> I got en error that I could not open scuba. Is this the correct way to go >> about this, or is there some other means that I should be doing not 'scuba'? >> >> Thank you, >> Anna >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 1:52 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> yes, create a volume ROI and you can map it onto the surface using >> mri_vol2surf >> >> cheers >> Bruce >> On Mon, 26 Sep 2016, Crawford, Anna wrote: >> >>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new >>> to this and am just trying to figure out how to get the basic process >>> first.) Eventually, I will want it related to another signal such as the >>> EEG from an epilepsy subject for example. In that case, it would be the >>> active region that I want to capture and then map it to the surface. First, >>> I want to be sure that I can get an ROI that I can then project to the >>> surface (which I assume would be something like mri_vol2surf) if that makes >>> sense. So i first need to be able to create the volume or label. >>> >>> Thank you, >>> Anna >>> >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 1:16 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> can you explain what the ROI is supposed to represent?
Re: [Freesurfer] Co-registering different source data
Hi, i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz among other similar variations. Am I just inputting it wrong or am I just missing information? Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data Hi Anna scuba is very old and deprecated. Try using freeview instead cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote: > To create the volume ROI, I found something that said to use: > > scuba -v $filename > > to then make a new ROI. > > I got en error that I could not open scuba. Is this the correct way to go > about this, or is there some other means that I should be doing not 'scuba'? > > Thank you, > Anna > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 1:52 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > yes, create a volume ROI and you can map it onto the surface using > mri_vol2surf > > cheers > Bruce > On Mon, 26 Sep 2016, Crawford, Anna wrote: > >> For now, I am just trying to get any arbitrary ROI that I define. (I'm new >> to this and am just trying to figure out how to get the basic process >> first.) Eventually, I will want it related to another signal such as the EEG >> from an epilepsy subject for example. In that case, it would be the active >> region that I want to capture and then map it to the surface. First, I want >> to be sure that I can get an ROI that I can then project to the surface >> (which I assume would be something like mri_vol2surf) if that makes sense. >> So i first need to be able to create the volume or label. >> >> Thank you, >> Anna >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 1:16 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> can you explain what the ROI is supposed to represent? If you can create >> it in the volume, you can use mri_vol2surf to map it onto the surface. >> >> cheers >> Bruce >> >> >> On Mon, 26 Sep 2016, Crawford, Anna wrote: >> >>> Hi, >>> >>> I am having trouble figuring out how to create my own ROI. I can visualize >>> the anatomical ROI created automatically. How do I create a new ROI? >>> >>> Thanks, >>> Anna >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 10:44 AM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> Hi Anna >>> >>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>> the white or pial surface, then you can visualize them on the inflated >>> surface trivially. That is, you can create your ROI on any surface of the >>> same hemisphere/subject and visualize it on any other >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Sep 2016, Crawford, Anna >>> wrote: >>> >>>> Hello, >>>> >>>> I am trying to create a new surface area on the inflated brain given by >>>> freesurfer >>>> using recon-all. I make to create my own ROI that is co-registered onto >>>> this surfer. >>>> Ultimately, I want to be able to take information from a different data >>>> source such as >>>> EEG and have it co-registered onto the inflated surface. How do I go about >>>> creating >>>>
Re: [Freesurfer] Co-registering different source data
To create the volume ROI, I found something that said to use: scuba -v $filename to then make a new ROI. I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data yes, create a volume ROI and you can map it onto the surface using mri_vol2surf cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote: > For now, I am just trying to get any arbitrary ROI that I define. (I'm new to > this and am just trying to figure out how to get the basic process first.) > Eventually, I will want it related to another signal such as the EEG from an > epilepsy subject for example. In that case, it would be the active region > that I want to capture and then map it to the surface. First, I want to be > sure that I can get an ROI that I can then project to the surface (which I > assume would be something like mri_vol2surf) if that makes sense. So i first > need to be able to create the volume or label. > > Thank you, > Anna > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 1:16 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > can you explain what the ROI is supposed to represent? If you can create > it in the volume, you can use mri_vol2surf to map it onto the surface. > > cheers > Bruce > > > On Mon, 26 Sep 2016, Crawford, Anna wrote: > >> Hi, >> >> I am having trouble figuring out how to create my own ROI. I can visualize >> the anatomical ROI created automatically. How do I create a new ROI? >> >> Thanks, >> Anna >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 10:44 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Hi Anna >> >> I'm not exactly sure what you mean, but if you register EEG electrodes to >> the white or pial surface, then you can visualize them on the inflated >> surface trivially. That is, you can create your ROI on any surface of the >> same hemisphere/subject and visualize it on any other >> >> cheers >> Bruce >> >> >> On Mon, 26 Sep 2016, Crawford, Anna >> wrote: >> >>> Hello, >>> >>> I am trying to create a new surface area on the inflated brain given by >>> freesurfer >>> using recon-all. I make to create my own ROI that is co-registered onto >>> this surfer. >>> Ultimately, I want to be able to take information from a different data >>> source such as >>> EEG and have it co-registered onto the inflated surface. How do I go about >>> creating >>> this new ROI surface? >>> >>> Thanks, >>> Anna >>> >>> === >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by >>> U.S.News & World >>> Report (2015). Visit us online at http://www.clevelandclinic.org for a >>> complete listing >>> of our services, staff and locations. Confidentiality Note: This message is >>> intended >>> for use only by the individual or entity to which it is addressed and may >>> contain >>> information that is privileged, confidential, and exempt from disclosure >>> under >>> applicable law. If the reader of this message is not the intended recipient >>> or the >>> employee or agent responsible for delivering the message to the intended >>> recipient, you >>> are hereby notified that any dissemination, distribution or copying of this >>> communication is strictly prohibited. If you have received this >>> communication in error, >>> please contact the sender immediately and destroy the material in its >>> entirety, whether >>> electronic or hard copy. Thank you. >>> >>&
Re: [Freesurfer] Co-registering different source data
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface. cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote: > Hi, > > I am having trouble figuring out how to create my own ROI. I can visualize > the anatomical ROI created automatically. How do I create a new ROI? > > Thanks, > Anna > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 10:44 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > I'm not exactly sure what you mean, but if you register EEG electrodes to > the white or pial surface, then you can visualize them on the inflated > surface trivially. That is, you can create your ROI on any surface of the > same hemisphere/subject and visualize it on any other > > cheers > Bruce > > > On Mon, 26 Sep 2016, Crawford, Anna > wrote: > >> Hello, >> >> I am trying to create a new surface area on the inflated brain given by >> freesurfer >> using recon-all. I make to create my own ROI that is co-registered onto this >> surfer. >> Ultimately, I want to be able to take information from a different data >> source such as >> EEG and have it co-registered onto the inflated surface. How do I go about >> creating >> this new ROI surface? >> >> Thanks, >> Anna >> >> === >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by >> U.S.News & World >> Report (2015). Visit us online at http://www.clevelandclinic.org for a >> complete listing >> of our services, staff and locations. Confidentiality Note: This message is >> intended >> for use only by the individual or entity to which it is addressed and may >> contain >> information that is privileged, confidential, and exempt from disclosure >> under >> applicable law. If the reader of this message is not the intended recipient >> or the >> employee or agent responsible for delivering the message to the intended >> recipient, you >> are hereby notified that any dissemination, distribution or copying of this >> communication is strictly prohibited. If you have received this >> communication in error, >> please contact the sender immediately and destroy the material in its >> entirety, whether >> electronic or hard copy. Thank you. >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > === > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News > & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of > our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the > individual or entity to which it
Re: [Freesurfer] Co-registering different source data
Hi, I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data Hi Anna I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote: > Hello, > > I am trying to create a new surface area on the inflated brain given by > freesurfer > using recon-all. I make to create my own ROI that is co-registered onto this > surfer. > Ultimately, I want to be able to take information from a different data > source such as > EEG and have it co-registered onto the inflated surface. How do I go about > creating > this new ROI surface? > > Thanks, > Anna > > === > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News > & World > Report (2015). Visit us online at http://www.clevelandclinic.org for a > complete listing > of our services, staff and locations. Confidentiality Note: This message is > intended > for use only by the individual or entity to which it is addressed and may > contain > information that is privileged, confidential, and exempt from disclosure under > applicable law. If the reader of this message is not the intended recipient > or the > employee or agent responsible for delivering the message to the intended > recipient, you > are hereby notified that any dissemination, distribution or copying of this > communication is strictly prohibited. If you have received this communication > in error, > please contact the sender immediately and destroy the material in its > entirety, whether > electronic or hard copy. Thank you. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Co-registering different source data
Hello, I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface? Thanks, Anna === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
