[Freesurfer] Upload the data in virtuell box!
Hello, I don't know how can I upload the DICOM Data in Virtuellbox.I installed the Virtuellbox in windows PC and would like to upload my Image but until now with out any sucsess. Should I install any extra programm to upload any files? Thanks for your Feedback. Best Regards Sarah ___ 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] mri_convert introduces flip
Hi experts, I´m trying to convert original images in native space from the LPBA40-Atlas (http://www.loni.ucla.edu/Atlases/LPBA40/) from img/hdr to nii/nii.gz. Conversion always results in a left/right flip. Also, mri_convert complains that no .mat file is available but there are no mat files provided... Here my command and output: mri_convert S01.native.mri.img S01.native.mri.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from S01.native.mri.img... - INFO: could not find /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file - TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to S01.native.mri.nii.gz... Thanks for your help, Janosch ___ 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] freesurfer license on multi-user cluster
Dear developers, I just installed freesurfer 5.1.0 system-wide on one of our clusters. All of our users can now access the software, although there is only one license key in the installation directory. Maybe you prefer that every user on our system uses their own license key for your usage statistics? An environment variable FREESURFER_LICENSE could maybe be used for this purpose? Or an additional check for a local license file ~/.freesurfer_license? With regards, John -- John Donners Consultant OSD SARA Science Park 140 1098 XG Amsterdam T +31 (0)20 592 3055 F +31 (0)20 668 3167 M +31 (0)6 1903 9023 E john.donn...@sara.nl www.sara.nl ___ 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] QDEC's clusters and connectivity maps
Dear FS team, I am trying to find what is the connection between white matter tracts with reduced FA and a number of cortical regions/clusters with significant reduction in cortical thickness from QDEC. Is there a way to overlap my cortical regions with reduced thickness more exactly the clusters from QDEC on the connectivity maps in FSL. How I create a mask of the QDEC clusters and used them in tractography? The tractography/ connectivity maps has been performed on the MNI standard space. Any suggestion will be greatly appreciated. Antonella ___ 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] freesurfer license on multi-user cluster
Hi John We prefer but don't require that every user download a license Thanks for asking Bruce On Aug 21, 2012, at 9:52 AM, John Donners john.donn...@sara.nl wrote: Dear developers, I just installed freesurfer 5.1.0 system-wide on one of our clusters. All of our users can now access the software, although there is only one license key in the installation directory. Maybe you prefer that every user on our system uses their own license key for your usage statistics? An environment variable FREESURFER_LICENSE could maybe be used for this purpose? Or an additional check for a local license file ~/.freesurfer_license? With regards, John -- John Donners Consultant OSD SARA Science Park 140 1098 XG Amsterdam T +31 (0)20 592 3055 F +31 (0)20 668 3167 M +31 (0)6 1903 9023 E john.donn...@sara.nl www.sara.nl ___ 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.
Re: [Freesurfer] Edits to aparc+aseg.mgz
Doug, Thanks for the update and not much time was wasted so no worries. I edited the brainmask.mgz file and ran the new recon-all command with autorecon-pial, which created a new brain.finalsurfs.mgz with the dura edited out and correct surfs. New stat files were created, but no new aparc+aseg.mgz file. Loading this file still shows the segmentation including dura in the cortex and the modification date is the original recon-all date. Is there any way to create a new aparc+aseg.mgz file with this new surf data? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 20, 2012 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, my apologies, I told you to edit the wrong file. You should edit brainmask.mgz, not brainmask.finalsurfs.mgz. Sorry about, I hope you did not waste too much time. doug On 08/20/2012 09:31 AM, Sarosh, Cyrus wrote: Doug, I edited the dura from the brain.finalsurfs.mgz file using the command tkmedit (subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going through the necessary slices that need fixing and erase the dura. I then ran this subject with the command recon-all -subjid (subject ID) -autorecon-pial. Looking at the date modified information it appears that new stat files were created, but no new aparc+aseg.mgz file was created. I loaded the brain.finalsurfs.mgz file, which contained a modify date of when I ran the new recon-all command and it looked identical to the original brain.finalsurfs.mgz file, so all of my edits were gone and all of the surfs were incorrect just like before. Also, loading the aparc+aseg.mgz file it looks identical to the previous aparc+aseg.mgz, so no changes were made. Looking at the log it appears my edits were useless because the first step that runs is the -maskbfs step which appears to generate the brain.finalsurfs.mgz file. So, do I need to edit a different file or was my command line incorrect? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 14, 2012 1:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz For GM volume and thickness, you will certainly want to fix it. Given how big the PET voxels are, it might not be such a big deal for that. To fix it, you would edit the dura from the brain.finalsurfs.mgz and run recon-all with -autorecon-pial. This will fix aparc+aseg and re-generate the stats files. doug On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote: Doug, Well we want to use the stats information for gray matter volume and thickness of certain vois and we want to use the aparc+aseg file to run PET image analysis to collect data from certain vois. Would performing the given actions correct any incorrect data in the stats files and create a new aparc+aseg.mgz file or will this require separate actions? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 14, 2012 11:28 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Depending upon how bad it is and what you are going to do with it, it may be a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run recon-all -autorecon-pial ... doug On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote: Doug, I looked at the surface files by using the command -tkmedit (subject ID) brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz file. The pial surface (red line) does identify the dura as part of the cortex, but it doesn't look as bad as the aseg.mgz vois made it appear. Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 13, 2012 4:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, this may or may not be a problem. The cortical label in aseg.mgz is not used for this reason. Usually, the surface-based method will exclude the dura in these situations. Are the surfaces accurate or are they including dura as well? BTW, you should not be editing the aparc+aseg.mgz. doug On 08/13/2012 01:04 PM, Sarosh, Cyrus wrote: Hello FreeSurfer Users, I looked for a possible solution to my problem in the Mail Archive and found this article referring to almost the exact same problem I am having: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314. h t ml. Basically,pieces of the subarachnoid space/pia mater/arachnoid/dura mater/skull are being
[Freesurfer] Convert QDEC clusters on the MNI_152_T1 space
Dear All, Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain template? Thank you. Antonella ___ 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] GCA file for non-human recon-all use
Hello, I have a few questions that I hope can be answered: Q1:How can '.label' files be turned into the necessary '.gca' file needed for the recon-all pipeline. Starting for the first step in auto-recon2.What else other than the '.label' files would be needed to create this '.gca' file? Q2: How to get the seg_edited.mgz file? I would want to use this file in the rebuild_gca_atas.csh script. Q3:Can the rebuild_gca_atlas.csh script be used to make a replacement for the RB_all_2008-03-26.gca file from the average folder? Q4:Is there a way to avoid needing the .gca file if cortical thickness measurements is the only goal?Or could there be a limited number of labels needed incorporated into the .gca file for this goal. Ex. Just Cerebral cortex ROI's. Thank you for any help, Jeff Thompson ___ 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] Upload the data in virtuell box!
Hi Sarah, I believe all you need to do is setup a shared directory between Windows (host OS) and Linux (guest OS - VirtualBox). Then you can copy your DICOM data to the shared folder and have access to it from within VirtualBox. Here are some directions which should help: http://www.virtualbox.org/manual/ch04.html#sharedfolders -Louis On Tue, 21 Aug 2012, Fouladi-Movahed, Sarah wrote: Hello, I don't know how can I upload the DICOM Data in Virtuellbox.I installed the Virtuellbox in windows PC and would like to upload my Image but until now with out any sucsess. Should I install any extra programm to upload any files? Thanks for your Feedback. Best Regards Sarah ___ 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.
[Freesurfer] mri_segstats error
Hi, I recently installed the updated mri_segstats (ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux). This seems to work fine for recalculating the supratentorial volume. However, it is causing my new recons to fail (see example error below). Any suggestions? Thanks, -Tyler $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24644/ones.mgz --i ./tmp.mri_nu_correct.mni.24644/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24644/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24644/output.mean.dat sysname Linux hostname login001 machine x86_64 user tblazey UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24644/ones.mgz Loading ./tmp.mri_nu_correct.mni.24644/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.24644/output.mean.dat (standard_in) 1: parse error The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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] Edits to aparc+aseg.mgz
Run it with -autorecon3 doug On 08/21/2012 10:44 AM, Sarosh, Cyrus wrote: Doug, Thanks for the update and not much time was wasted so no worries. I edited the brainmask.mgz file and ran the new recon-all command with autorecon-pial, which created a new brain.finalsurfs.mgz with the dura edited out and correct surfs. New stat files were created, but no new aparc+aseg.mgz file. Loading this file still shows the segmentation including dura in the cortex and the modification date is the original recon-all date. Is there any way to create a new aparc+aseg.mgz file with this new surf data? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 20, 2012 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, my apologies, I told you to edit the wrong file. You should edit brainmask.mgz, not brainmask.finalsurfs.mgz. Sorry about, I hope you did not waste too much time. doug On 08/20/2012 09:31 AM, Sarosh, Cyrus wrote: Doug, I edited the dura from the brain.finalsurfs.mgz file using the command tkmedit (subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going through the necessary slices that need fixing and erase the dura. I then ran this subject with the command recon-all -subjid (subject ID) -autorecon-pial. Looking at the date modified information it appears that new stat files were created, but no new aparc+aseg.mgz file was created. I loaded the brain.finalsurfs.mgz file, which contained a modify date of when I ran the new recon-all command and it looked identical to the original brain.finalsurfs.mgz file, so all of my edits were gone and all of the surfs were incorrect just like before. Also, loading the aparc+aseg.mgz file it looks identical to the previous aparc+aseg.mgz, so no changes were made. Looking at the log it appears my edits were useless because the first step that runs is the -maskbfs step which appears to generate the brain.finalsurfs.mgz file. So, do I need to edit a different file or was my command line incorrect? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 14, 2012 1:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz For GM volume and thickness, you will certainly want to fix it. Given how big the PET voxels are, it might not be such a big deal for that. To fix it, you would edit the dura from the brain.finalsurfs.mgz and run recon-all with -autorecon-pial. This will fix aparc+aseg and re-generate the stats files. doug On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote: Doug, Well we want to use the stats information for gray matter volume and thickness of certain vois and we want to use the aparc+aseg file to run PET image analysis to collect data from certain vois. Would performing the given actions correct any incorrect data in the stats files and create a new aparc+aseg.mgz file or will this require separate actions? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 14, 2012 11:28 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Depending upon how bad it is and what you are going to do with it, it may be a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run recon-all -autorecon-pial ... doug On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote: Doug, I looked at the surface files by using the command -tkmedit (subject ID) brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz file. The pial surface (red line) does identify the dura as part of the cortex, but it doesn't look as bad as the aseg.mgz vois made it appear. Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 13, 2012 4:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, this may or may not be a problem. The cortical label in aseg.mgz is not used for this reason. Usually, the surface-based method will exclude the dura in these situations. Are the surfaces accurate or are they including dura as well? BTW, you should not be editing the aparc+aseg.mgz. doug On 08/13/2012 01:04 PM, Sarosh, Cyrus wrote: Hello FreeSurfer Users, I looked for a possible solution to my problem in the Mail Archive and found this article referring to almost the exact same problem I am having: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314. h t ml.
Re: [Freesurfer] mri_segstats error
Sorry, there was a bug in that version. I've put an updated version on that ftp site doug On 08/21/2012 03:49 PM, Blazey, Tyler wrote: Hi, I recently installed the updated mri_segstats (ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux). This seems to work fine for recalculating the supratentorial volume. However, it is causing my new recons to fail (see example error below). Any suggestions? Thanks, -Tyler $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24644/ones.mgz --i ./tmp.mri_nu_correct.mni.24644/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24644/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24644/output.mean.dat sysname Linux hostname login001 machine x86_64 user tblazey UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24644/ones.mgz Loading ./tmp.mri_nu_correct.mni.24644/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.24644/output.mean.dat (standard_in) 1: parse error The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] GCA file for non-human recon-all use
1. These need to be image volumes with every voxel containing an index into FreeSurferColorLUT.txt 2. Use the volumes from 1. 3. Yes. 4. The aseg is used to automated several steps in cortical surface reconning that you will need to do manually if you don't have one (ventricle/thalamus/basal ganglia filling, removing brainstem and cerebellum, spackling white matter inferior to hippocampus, etc) cheers Bruce On Tue, 21 Aug 2012, Jeff Thompson wrote: Hello, I have a few questions that I hope can be answered: Q1: How can '.label' files be turned into the necessary '.gca' file needed for the recon-all pipeline. Starting for the first step in auto-recon2. What else other than the '.label' files would be needed to create this '.gca' file? Q2: How to get the seg_edited.mgz file? I would want to use this file in the rebuild_gca_atas.csh script. Q3: Can the rebuild_gca_atlas.csh script be used to make a replacement for the RB_all_2008-03-26.gca file from the average folder? Q4: Is there a way to avoid needing the .gca file if cortical thickness measurements is the only goal? Or could there be a limited number of labels needed incorporated into the .gca file for this goal. Ex. Just Cerebral cortex ROI's. Thank you for any help, Jeff Thompson ___ 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] bbregister with PET data
Hi Marco, I think it might be that your PET volume is left-right reversed. I reran bbregister after left-right reversing the pet data and it looks much better. mri_convert PBR_CLBP001_average8-28_BET_hdrOK.nii --left-right-reverse-pix lrrev.nii There's always the chance that the T1 was reversed, but I suspect the PET :). doug On 08/20/2012 11:36 PM, Marco Loggia, PhD wrote: Hi Doug and Freesurfer team, I am trying to coregister some PET maps with their relative high resolution MEMPRAGE files. I was thinking that bbregister might be my best option but the results are still not satisfactory, likely due to the intrinsic features of my radioligand (the resulting maps are quite 'noisy' in terms of anatomical details). Do you have any suggestions on how to improve the results of bbregister (e.g., flags to use, or preprocessing steps prior to running bbregister)? -the PET map for one subject is here: /autofs/space/katahdin_005/users/marco/PBR28/data/PBR_CLBP001/PET/PBR_CLBP001_average8-28_BET_hdrOK.nii -my SUBJECTS_DIR is here /autofs/space/katahdin_005/users/marco/PBR28/data/ - The command I ran is: bbregister --init-fsl --mov PBR_CLBP001_average8-28_BET_hdrOK.nii --t2 --s PBR_CLBP001 --reg PET2brain.BB.reg --o PET2brain.BB.nii Thanks! Marco __ Marco L. Loggia, PhD Postdoctoral Fellow Massachusetts General Hospital Brigham and Women's Hospital Harvard Medical School 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 ma...@nmr.mgh.harvard.edu mailto:ma...@nmr.mgh.harvard.edu ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Convert QDEC clusters on the MNI_152_T1 space
You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat doug On 08/21/2012 11:06 AM, Antonella Kis wrote: Dear All, Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain template? Thank you. Antonella ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] cortical surface area related measures
Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al 4. roi based, i.e. based on the surface areas of the parcellation units in lh.aparc.a2009s.stats etc. 1. recent pub, Lisa T. Eyler et. al used the areal expansion method. was this done exactly as would be achived by using the area tab on qdec and setting up a glm ? Dale published surface area specifying some details of implementation but i was not sure if this was exactly what is implemented in qdec ? 2. LGI seems to me this is the ratio of two areas, that of the hull to the area inscribed by projecting the border of the hull onto the grey/white surface. In an e-mail Nick said LGI is a curvature based measure and that confused me a bit. gyrification is of course related to curvature but it seems the quantities actually calculated here are ratios of areas, which gives local info on surface area differences. 3. the winkler stuff is i think not publicly available yet at this time ? 4. straightforward enough not withstanding ICV corrections, etc. any words of clarification before i start trying some analysis on my group ? thank you Greg ___ 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] cortical surface area related measures
Hi Greg, I don't know what areal expansion refers to. If you want to use area (eg, the area tab in qdec), you should make sure to download the most recent version of mris_preproc (which performs a jacobian type correction) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc doug On 08/21/2012 04:59 PM, Gregory Kirk wrote: Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al 4. roi based, i.e. based on the surface areas of the parcellation units in lh.aparc.a2009s.stats etc. 1. recent pub, Lisa T. Eyler et. al used the areal expansion method. was this done exactly as would be achived by using the area tab on qdec and setting up a glm ? Dale published surface area specifying some details of implementation but i was not sure if this was exactly what is implemented in qdec ? 2. LGI seems to me this is the ratio of two areas, that of the hull to the area inscribed by projecting the border of the hull onto the grey/white surface. In an e-mail Nick said LGI is a curvature based measure and that confused me a bit. gyrification is of course related to curvature but it seems the quantities actually calculated here are ratios of areas, which gives local info on surface area differences. 3. the winkler stuff is i think not publicly available yet at this time ? 4. straightforward enough not withstanding ICV corrections, etc. any words of clarification before i start trying some analysis on my group ? thank you Greg ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] freesurfer license on multi-user cluster (Bruce Fischl)
Hi, Bruce, I'm wondering where I can get this system-wide FreeSurfer 5.1 download? Also, is there any manual or instruction for installation on multi-user clusters? Thank you very much! Zheng Wang -邮件原件- 发件人: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 freesurfer-request@nmr. mgh.harvard.edu 发送时间: 2012年8月22日 0:00 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Freesurfer Digest, Vol 102, Issue 23 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than Re: Contents of Freesurfer digest... Today's Topics: 1. mri_convert introduces flip (Janosch Linkersd?rfer) 2. freesurfer license on multi-user cluster (John Donners) 3. QDEC's clusters and connectivity maps (Antonella Kis) 4. Re: freesurfer license on multi-user cluster (Bruce Fischl) 5. Re: Edits to aparc+aseg.mgz (Sarosh, Cyrus) 6. Convert QDEC clusters on the MNI_152_T1 space (Antonella Kis) -- Message: 1 Date: Tue, 21 Aug 2012 13:42:43 +0200 From: Janosch Linkersd?rfer notes4ja...@googlemail.com Subject: [Freesurfer] mri_convert introduces flip To: freesurfer freesurfer@nmr.mgh.harvard.edu Message-ID: bc636725-64b9-4919-b13d-a270261a1...@googlemail.com Content-Type: text/plain; charset=iso-8859-1 Hi experts, I?m trying to convert original images in native space from the LPBA40-Atlas (http://www.loni.ucla.edu/Atlases/LPBA40/) from img/hdr to nii/nii.gz. Conversion always results in a left/right flip. Also, mri_convert complains that no .mat file is available but there are no mat files provided... Here my command and output: mri_convert S01.native.mri.img S01.native.mri.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from S01.native.mri.img... - INFO: could not find /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file - TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to S01.native.mri.nii.gz... Thanks for your help, Janosch -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20120821/9a 5f1637/attachment-0001.html -- Message: 2 Date: Tue, 21 Aug 2012 15:52:00 +0200 From: John Donners john.donn...@sara.nl Subject: [Freesurfer] freesurfer license on multi-user cluster To: freesurfer@nmr.mgh.harvard.edu Message-ID: 50339280.3020...@sara.nl Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear developers, I just installed freesurfer 5.1.0 system-wide on one of our clusters. All of our users can now access the software, although there is only one license key in the installation directory. Maybe you prefer that every user on our system uses their own license key for your usage statistics? An environment variable FREESURFER_LICENSE could maybe be used for this purpose? Or an additional check for a local license file ~/.freesurfer_license? With regards, John -- John Donners Consultant OSD SARA Science Park 140 1098 XG Amsterdam T +31 (0)20 592 3055 F +31 (0)20 668 3167 M +31 (0)6 1903 9023 E john.donn...@sara.nl www.sara.nl -- Message: 3 Date: Tue, 21 Aug 2012 07:04:48 -0700 (PDT) From: Antonella Kis ator...@yahoo.com Subject: [Freesurfer] QDEC's clusters and connectivity maps To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: 1345557888.55711.yahoomail...@web121701.mail.ne1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear FS team, I am trying to find what is the? connection between white matter tracts with reduced FA and a number of cortical regions/clusters with significant reduction in cortical thickness from QDEC. Is there a way to overlap my cortical regions with reduced thickness more exactly the clusters from QDEC on the connectivity maps in FSL. How I create a mask of the QDEC clusters and used them in tractography?? The tractography/ connectivity maps has been performed on the MNI standard space. Any suggestion will be greatly appreciated. Antonella -- next part -- An HTML attachment
Re: [Freesurfer] freesurfer license on multi-user cluster (Bruce Fischl)
Hi Zheng no, not really. In general if you have multiple users we would request that they each get a license even if they don't use it so that we can get a reasonably accurate accounting of how many users we have, but we don't require anything other than that our binaries can find the license file when they execute. cheers Bruce On Wed, 22 Aug 2012, Wang, Zheng wrote: Hi, Bruce, I'm wondering where I can get this system-wide FreeSurfer 5.1 download? Also, is there any manual or instruction for installation on multi-user clusters? Thank you very much! Zheng Wang -- ???: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] ?? freesurfer-request@nmr. mgh.harvard.edu : 2012?8?22? 0:00 ???: freesurfer@nmr.mgh.harvard.edu ??: Freesurfer Digest, Vol 102, Issue 23 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than Re: Contents of Freesurfer digest... Today's Topics: 1. mri_convert introduces flip (Janosch Linkersd?rfer) 2. freesurfer license on multi-user cluster (John Donners) 3. QDEC's clusters and connectivity maps (Antonella Kis) 4. Re: freesurfer license on multi-user cluster (Bruce Fischl) 5. Re: Edits to aparc+aseg.mgz (Sarosh, Cyrus) 6. Convert QDEC clusters on the MNI_152_T1 space (Antonella Kis) -- Message: 1 Date: Tue, 21 Aug 2012 13:42:43 +0200 From: Janosch Linkersd?rfer notes4ja...@googlemail.com Subject: [Freesurfer] mri_convert introduces flip To: freesurfer freesurfer@nmr.mgh.harvard.edu Message-ID: bc636725-64b9-4919-b13d-a270261a1...@googlemail.com Content-Type: text/plain; charset=iso-8859-1 Hi experts, I?m trying to convert original images in native space from the LPBA40-Atlas (http://www.loni.ucla.edu/Atlases/LPBA40/) from img/hdr to nii/nii.gz. Conversion always results in a left/right flip. Also, mri_convert complains that no .mat file is available but there are no mat files provided... Here my command and output: mri_convert S01.native.mri.img S01.native.mri.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from S01.native.mri.img... - INFO: could not find /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file - TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to S01.native.mri.nii.gz... Thanks for your help, Janosch -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20120821/9a 5f1637/attachment-0001.html -- Message: 2 Date: Tue, 21 Aug 2012 15:52:00 +0200 From: John Donners john.donn...@sara.nl Subject: [Freesurfer] freesurfer license on multi-user cluster To: freesurfer@nmr.mgh.harvard.edu Message-ID: 50339280.3020...@sara.nl Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear developers, I just installed freesurfer 5.1.0 system-wide on one of our clusters. All of our users can now access the software, although there is only one license key in the installation directory. Maybe you prefer that every user on our system uses their own license key for your usage statistics? An environment variable FREESURFER_LICENSE could maybe be used for this purpose? Or an additional check for a local license file ~/.freesurfer_license? With regards, John ___ 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.
