[Freesurfer] repeat: trouble loading nifti files
Hi All, I am re-posting this question since there was no response to my previous attempt. I have a problem conforming certain nifti files, the following is the log when i try to convert them, reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... INFO: using NIfTI-1 qform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -4.99113e-10, -1) j_ras = (-4.99113e-10, -1, 4.99113e-10) k_ras = (-1, 4.99113e-10, 0) WARNING ===== The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 282 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ===== Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 282 voxels for all directions Reslicing using nearest This is understood, however I want them to be conformed to 256^3 mm. If I use -cs 256 flag, it does resample the image to 256^3mm but the image is blank. Is there something wrong I am doing? How do I conform these files to 256^3mm? Any help will be greatly appreciated. Best, Akshay ___ 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] repeat: trouble loading nifti files
Hi Akshay is you send us that file we'll take a look. cheers Bruce On Tue, 7 May 2013, Akshay wrote: Hi All, I am re-posting this question since there was no response to my previous attempt. I have a problem conforming certain nifti files, the following is the log when i try to convert them, reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... INFO: using NIfTI-1 qform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -4.99113e-10, -1) j_ras = (-4.99113e-10, -1, 4.99113e-10) k_ras = (-1, 4.99113e-10, 0) WARNING ===== The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 282 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ===== Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 282 voxels for all directions Reslicing using nearest This is understood, however I want them to be conformed to 256^3 mm. If I use -cs 256 flag, it does resample the image to 256^3mm but the image is blank. Is there something wrong I am doing? How do I conform these files to 256^3mm? Any help will be greatly appreciated. Best, Akshay ___ 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] Fwd: Re: repeat: trouble loading nifti files
mri_convert path-to-nifti file mask.mgz --resample_type nearest -cs 256 On 5/7/13 2:55 PM, Bruce Fischl wrote: can you send me the full mri_convert command line that is run? On Tue, 7 May 2013, Akshay wrote: Hi Bruce Please find the file attached Best, Akshay On 5/7/13 2:40 PM, Bruce Fischl wrote: Hi Akshay is you send us that file we'll take a look. cheers Bruce On Tue, 7 May 2013, Akshay wrote: Hi All, I am re-posting this question since there was no response to my previous attempt. I have a problem conforming certain nifti files, the following is the log when i try to convert them, reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... INFO: using NIfTI-1 qform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -4.99113e-10, -1) j_ras = (-4.99113e-10, -1, 4.99113e-10) k_ras = (-1, 4.99113e-10, 0) WARNING ===== The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 282 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ===== Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 282 voxels for all directions Reslicing using nearest This is understood, however I want them to be conformed to 256^3 mm. If I use -cs 256 flag, it does resample the image to 256^3mm but the image is blank. Is there something wrong I am doing? How do I conform these files to 256^3mm? Any help will be greatly appreciated. Best, Akshay ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all completes without all the info..
On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote: Hi, This is a new issue as it used to run well before.. I run recon-all ... ... -autorecon1 - force and it completes without error but I don't have all the files.. Attached is a screenshot. On the right is the output from a file that worked before and on the left is a newer folder.. Screenshot.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 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] TrackVis either end command
Dear Freesurfer/TrackVis experts, I am using the following command in a batchfile to identify tracks counts between dozens of preset ROIs. track_vis DATAPATHtob0.trk -roi DATAPATHTOROI1.nii -roi2 DATAPATHTOROI2.nii -o PATHTOOUTPUT.trk OUTPUT.txt -nr', i, j, i, j, i, j Is there a line command I can use so that the tracks identified follow the rule either end in the ROIs instead of the default any part? Thank you! Cat ___ 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] TrackVis either end command
Hi Catherine, This question might not fit in freesurfer mailing list but I'll answer here anyway - Unfortunately, for the command-line track_vis, there is no such option. Ruopeng On May 7, 2013, at 9:53 AM, Chu, Catherine,M.D. cc...@partners.org wrote: Dear Freesurfer/TrackVis experts, I am using the following command in a batchfile to identify tracks counts between dozens of preset ROIs. track_vis DATAPATHtob0.trk -roi DATAPATHTOROI1.nii -roi2 DATAPATHTOROI2.nii -o PATHTOOUTPUT.trk OUTPUT.txt -nr', i, j, i, j, i, j Is there a line command I can use so that the tracks identified follow the rule either end in the ROIs instead of the default any part? Thank you! Cat ___ 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] Fwd: Re: repeat: trouble loading nifti files
Hi Akshay the -cs flag specifies the voxel size, not the field of view, so you are creating a volume with 256mm voxels! Try --cw256 instead. cheers Bruce On Tue, 7 May 2013, Akshay wrote: mri_convert path-to-nifti file mask.mgz --resample_type nearest -cs 256 On 5/7/13 2:55 PM, Bruce Fischl wrote: can you send me the full mri_convert command line that is run? On Tue, 7 May 2013, Akshay wrote: Hi Bruce Please find the file attached Best, Akshay On 5/7/13 2:40 PM, Bruce Fischl wrote: Hi Akshay is you send us that file we'll take a look. cheers Bruce On Tue, 7 May 2013, Akshay wrote: Hi All, I am re-posting this question since there was no response to my previous attempt. I have a problem conforming certain nifti files, the following is the log when i try to convert them, reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... INFO: using NIfTI-1 qform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -4.99113e-10, -1) j_ras = (-4.99113e-10, -1, 4.99113e-10) k_ras = (-1, 4.99113e-10, 0) WARNING ===== The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 282 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ===== Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 282 voxels for all directions Reslicing using nearest This is understood, however I want them to be conformed to 256^3 mm. If I use -cs 256 flag, it does resample the image to 256^3mm but the image is blank. Is there something wrong I am doing? How do I conform these files to 256^3mm? Any help will be greatly appreciated. Best, Akshay ___ 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 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
Re: [Freesurfer] recon-all completes without all the info..
Hi Sudhin, You'll need to also run -autorecon2 and -autorecon3 in order to get surfaces and all the cortical/sub-cortical measures. -Louis On Tue, 7 May 2013, Sudhin A. Shah wrote: On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote: Hi, This is a new issue as it used to run well before.. I run recon-all ... ... -autorecon1 - force and it completes without error but I don't have all the files.. Attached is a screenshot. On the right is the output from a file that worked before and on the left is a newer folder.. Screenshot.png___ 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 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] segfault during rfx with mri_glmfit
hi freesurfers, i am running into a segfault whenever i try to use mri_glmfit to run a random effects analysis. (this is in the volume, not on the surface.) here's my call: mri_glmfit \ --y $ces_fpath \ --X $design_mat_fpath \ --C $c1_fpath \ --C $c2_fpath \ --C $c3_fpath \ --mask $mask_fpath \ --glmdir $glmdir_fpath \ --nii.gz i've tried a number of things to reduce the memory footprint of the call: -- originally i was using WLS, but i was worried about the memory demands of the cesvar, so i switched to OLS -- i introduced a GM mask -- i downsampled the ces and cesvar images (from 1 mm isotropic [cvs space] to 2 mm isotropic) any thoughts on what could be going wrong here? thanks, guys! alex ps. below are my build stamp, my info dump from mri_glmfit, and an example stderr stdout. my fs build stamp: freesurfer-Linux-centos4_x86_64-dev-20120104 the all info dump from mri_glmfit: ProgramName: mri_glmfit ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2013/05/07-14:15:28-GMT BuildTimeStamp: Jan 4 2012 05:11:02 CVS: $Id: mri_glmfit.c,v 1.209 2011/12/16 19:02:28 greve Exp $ User: alexkell Machine: ba7 Platform: Linux PlatformVersion: 2.6.38-16-generic CompilerName: GCC CompilerVersion: 30400 an example stderr and stdout: $Id: mri_glmfit.c,v 1.209 2011/12/16 19:02:28 greve Exp $ cwd /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_output/F-O cmdline mri_glmfit --y /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz --wls /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.cesvar.F-O.runs_1234.2x2x2.nii.gz --X /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//design_matrix.dat --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//asd.mtx --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//tc.mtx --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//tc-asd.mtx --mask /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input/cvs.gmMask.2x2x2.nii.gz --glmdir /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O --yhat-save --eres-save --save-cond --nii.gz sysname Linux hostname ba7 machine x86_64 user alexkell FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_input/cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz logyflag 0 X /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//design_matrix.dat usedti 0 mask /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input/cvs.gmMask.2x2x2.nii.gz maskinv 0 glmdir /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O IllCondOK 0 ReScaleX 1 DoFFx 0 wFile /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.cesvar.F-O.runs_1234.2x2x2.nii.gz weightinv 1 weightsqrt 1 Creating output directory /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O Loading y from /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_input/cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz Saving design matrix to /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O/Xg.dat Normalized matrix condition is 1 Matrix condition is 2.21429 Pruning voxels by thr: 0.00 Found 115353 voxels in mask Saving mask to /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O/mask.nii.gz search space = 922824.00 Segmentation fault ___ 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 analysis for only particular regions of interest?
Hello, I'm new to Freesurfer and I was wondering whether anybody could tell me what steps I need to do in Freesurfer in order to conduct the following analysis? I would like to know which sex differences in cortical thickness (subjects 12-18 years old) are present in the 12 year olds already. I've used qdec to calculate the main effect of sex in a) all participants (12-18) and b) in 12 year olds. Is there a way how to mask the 12-year olds' results with the whole group so that I can calculate which of the whole-group main effects are present before the age of 13? Thanks a lot for any suggestions, Klara ___ 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] NFS v4 on CentOS 5.4 or Red Hat 6.2
Hi FS experts, we have changed our file systems to NFS v4 and we found that FS cannot write to it (I mean, FS installed in an app server and subjects in the file system is not working). Last new I have is that FS in CentOS could read but not write and in Red Hat could not write or read. Is it a known problem? Is it something going on with FS or the problem is in our end? (the rest of the programs are working fine: FSL, Matlab...) Many thanks, Gari ___ 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] Segmentation fault (core dumped) again in the BETA version
Hi Freesurfer experts, I've got Ubuntu version 13.04 installed on my computer, and after I saw the post : http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html; I d ecide to install the BETA version freesurfer-Linux-centos6_x86_64-stable-pub-v5. 3.0-BETA.tar.gz as adviced. I still run into the same error when I run mri_nu_correct.mni and tkmedit: Segmentation fault (core dumped) ERROR: converting to minc and === ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... : Can anyone please advice on that? thanks a lot Martina ___ 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] Neuroimaging Research Technician
* * * * ** *A Neuroimaging Research Technician position is available in the VA Boston Healthcare System (VABHS) Neuroimaging Research for Veterans (NeRVe) Center. * * The Neuroimaging Research Technician will provide technical support for image preprocessing and analysis (using programs such as FSL and FreeSurfer), maintenance and development of in-house custom processing codes (script writing in unix/linux, matlab, etc), and assist staff members in the conduct of neuroimaging research as well as administrative tasks related to the Center. This includes developing expertise and training other investigators with the operation of current MRI hardware (scanner console, goggles, headphones, BioPac system, etc) and software for data processing and analysis. Additional responsibilities will include management of online documentation and center resources. Technical skills and familiarity with Linix/Unix, Matlab, and imaging software packages such as FSL and FreeSurfer is beneficial. Applicants should have a minimum of a Bachelor’s degree, with a background in Neuroscience, Computer Science, Engineering, Math or Physics. A two year commitment is required. Must be a U.S. citizen. Interested candidates should email a cover letter, resume, and contact information for two professional references to Emily Lindemer at emily.linde...@va.gov . * ___ 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] recon-all completes without all the info..
Is there 1 command line? I used to just run the 1 line. On May 7, 2013, at 10:19 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Sudhin, You'll need to also run -autorecon2 and -autorecon3 in order to get surfaces and all the cortical/sub-cortical measures. -Louis On Tue, 7 May 2013, Sudhin A. Shah wrote: On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote: Hi, This is a new issue as it used to run well before.. I run recon-all ... ... -autorecon1 - force and it completes without error but I don't have all the files.. Attached is a screenshot. On the right is the output from a file that worked before and on the left is a newer folder.. Screenshot.png___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all completes without all the info..
Yes, the -all flag will run autorecon1, autorecon2, and autorecon3. recon-all -all -i path to dicom/nii/mgz T1 image -s subjID For that uncompleted subject you have though if sounds like you just need to run autorecon2 and 3 recon-all -autorecon2 -autorecon3 -s subjID On Tue, 7 May 2013, Sudhin A. Shah wrote: Is there 1 command line? I used to just run the 1 line. On May 7, 2013, at 10:19 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Sudhin, You'll need to also run -autorecon2 and -autorecon3 in order to get surfaces and all the cortical/sub-cortical measures. -Louis On Tue, 7 May 2013, Sudhin A. Shah wrote: On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote: Hi, This is a new issue as it used to run well before.. I run recon-all ... ... -autorecon1 - force and it completes without error but I don't have all the files.. Attached is a screenshot. On the right is the output from a file that worked before and on the left is a newer folder.. Screenshot.png___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
Hi Nick, hi List, I have been having the exact same problem (also posted it on this list) with every freesurfer version on Opensuse 12.3, and haven't been able to sort it out. Any luck with it? Any pointers would be highly appreciated. Thanks in advance, Nicola On 5/1/2013 4:42 PM, Nick Jones wrote: Hi, I've run into a license problem with the latest version of Freesurfer on OpenSuse 12.3. 64 bit. FREESURFER_HOME: /usr/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Kernel info: Linux 3.7.10-1.1-desktop x86_64 When running a test: /usr/freesurferecho $shell /bin/tcsh /usr/freesurfersource SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/freesurfer FSFAST_HOME /usr/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/freesurfer/subjects MNI_DIR /usr/freesurfer/mni FSL_DIR /usr/fsl /usr/freesurfertkmedit bert orig.mgz -- ERROR: Invalid FreeSurfer license key found in license file /usr/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- /usr/freesurfercat .license hotm...@hotmail.com 14743 *C5.JPynIz8mt /usr/freesurfer This license file has been obfuscated. /usr/freesurferll -a .license -rw-r--r-- 1 root root 46 Apr 29 09:38 .license /usr/freesurfercat VERSION freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 /usr/freesurferzypper targetos openSUSE-12.3-x86_64 /usr/freesurferuname -a Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC 2013 (82d3f21) x86_64 x86_64 x86_64 GNU/Linux Name: tcl Version: 8.5.12-3.1.3 Name: tk Version: 8.5.12-3.1.1 Thanks to anyone who can provide some insight or workaround. I'm also curious if anyone knows the reasoning behind using this type of license mechanism, as opposed to agreeing to a license prior to downloading, like FSL or 3DSlicer? Nick ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
Nicola and Nick, Can you try the tkmedit.bin found here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ copy it to the freesurfer/tktools directory (the wrapper script 'tkmedit' in the bin dir calls the binary in the tktools dir). I'm hoping the problem you are seeing is the same one that others have seen on Fedora 19 and Ubuntu 13 which is fixed for the upcoming 5.3 release. Nick On Tue, 2013-05-07 at 12:15 -0400, Nicola Toschi wrote: Hi Nick, hi List, I have been having the exact same problem (also posted it on this list) with every freesurfer version on Opensuse 12.3, and haven't been able to sort it out. Any luck with it? Any pointers would be highly appreciated. Thanks in advance, Nicola On 5/1/2013 4:42 PM, Nick Jones wrote: Hi, I've run into a license problem with the latest version of Freesurfer on OpenSuse 12.3. 64 bit. FREESURFER_HOME: /usr/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Kernel info: Linux 3.7.10-1.1-desktop x86_64 When running a test: /usr/freesurferecho $shell /bin/tcsh /usr/freesurfersource SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/freesurfer FSFAST_HOME /usr/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/freesurfer/subjects MNI_DIR /usr/freesurfer/mni FSL_DIR /usr/fsl /usr/freesurfertkmedit bert orig.mgz -- ERROR: Invalid FreeSurfer license key found in license file /usr/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- /usr/freesurfercat .license hotm...@hotmail.com 14743 *C5.JPynIz8mt /usr/freesurfer This license file has been obfuscated. /usr/freesurferll -a .license -rw-r--r-- 1 root root 46 Apr 29 09:38 .license /usr/freesurfercat VERSION freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 /usr/freesurferzypper targetos openSUSE-12.3-x86_64 /usr/freesurferuname -a Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC 2013 (82d3f21) x86_64 x86_64 x86_64 GNU/Linux Name: tcl Version: 8.5.12-3.1.3 Name: tk Version: 8.5.12-3.1.1 Thanks to anyone who can provide some insight or workaround. I'm also curious if anyone knows the reasoning behind using this type of license mechanism, as opposed to agreeing to a license prior to downloading, like FSL or 3DSlicer? Nick ___ 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 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
Re: [Freesurfer] Segmentation fault (core dumped) again in the BETA version
Martina, Can you send me the recon-all.log file? Nick On Tue, 2013-05-07 at 17:38 +0200, martina.andell...@fastwebnet.it wrote: Hi Freesurfer experts, I've got Ubuntu version 13.04 installed on my computer, and after I saw the post : http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html; I d ecide to install the BETA version freesurfer-Linux-centos6_x86_64-stable-pub-v5. 3.0-BETA.tar.gz as adviced. I still run into the same error when I run mri_nu_correct.mni and tkmedit: Segmentation fault (core dumped) ERROR: converting to minc and === ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... : Can anyone please advice on that? thanks a lot Martina ___ 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] Issues with Cluster generation
Hi Joshua, there are several issues. First, you are using a threshold of p.0001 which is pretty severe. It works for the tutorial, but you need to understand what this threshold is and pick one appropriate for your data. Second, you are only doing 5 iterations. You need to be doing something like 1. If you are doing a whole cortex analysis, you can use the cached table instead of doing a simulation (with --qache). Running your own simulation will take a long time. The smoothing level is a little high, I usually run at 10 or 15. There's nothing wrong, it is just a little high. doug On 05/05/2013 03:39 AM, Joshua deSouza wrote: Hi Doug, The image has undergone fwhm 20 smoothing. The final glmdir file is given in the attachments. RC.txt was the contrast name and folder in which the cluster correction files are kept. The glmdir creation command line : mri_glmfir --y lh.thomasR.20.mgh --fsgd R.txt dods --C RC.txt --surf fsaverage lh --cortex --glmdir lh.thomasR.glmdir The glmfit-sim command line is : mri_glmfit-sim --glmdir lh.thomasR.glmdir --sim mc-z 5 4 mc-z.negative --sim-sign neg --cwpvalthresh 0.999 --overwrite The command line to view the image is : tksurfer fsaverage lh inflated -annot lh.thomasR.glmdir/RC.txt/mz-z.negative.sig.ocn.annot fthresh 1 -curv -gray The version of freesufrer i'm using is 1.379.2.17 Thank you helping me out with this. On Sat, May 4, 2013 at 12:12 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you send the command line and terminal output and the version of FS you are using? doug On 05/03/2013 09:01 AM, Joshua deSouza wrote: Hello all, I am facing a problem whereby after running GLMfit and cluserwise correction for multiple comparisons using the monte-carlo method, I was unable to generate any clusters. I do have significant images produced for the glmfit. All procedures were done according to the tutorial to match the effects under FSGD. There are no clusters available even when I set the cwpvalthresh to .999 which is supposed to show all clusters. What is the cluster generation dependent upon? As my glmfit does show significant areas. Please advise ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 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. -- 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
Re: [Freesurfer] ROI analyses
On 05/07/2013 05:21 AM, Tudor Popescu wrote: Hi Doug, I was just wondering whether you received my last email, with follow-ups on your answers. Sorry for the multitude of questions - as ever, I really appreciate the help! Best wishes, Tudor On 4 May 2013 20:31, Tudor Popescu tud...@gmail.com mailto:tud...@gmail.com wrote: Sorry Doug, wasn't sure whether you'd seen my reply Tudor -- Forwarded message -- From: *Tudor Popescu* tud...@gmail.com mailto:tud...@gmail.com Date: 2 May 2013 21:54 Subject: Re: [Freesurfer] ROI analyses To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Thanks Doug! If I may follow up: 3) (I can't see whether there's a tutorial for this, as the main FS site seems to be down at the moment) How can a group comparison of CT be done inside a given ROI, and in what ways can the ROI be specified? I guess the command line version of QDEC would produce, in this case, the same contrasts as QDEC, but within the ROI as opposed to the whole brain You mean you want to do an exploratory analysis within a mask of an ROI or that you want to average the CT scan within the ROI and do a group analysis of the ROI values? If the former, you can use mri_glmfit with the -label or -mask option. If the latter, you can create a table with asegstats2table then run mri_glmfit with --table 3') Is it the case that mri_glmfit with mask=brainmask.mgz is equivalent to doing a whole-brain analysis in QDEC? QDEC is only doing surface-based analysis. brainmask.mgz is a volume. But in principle the idea is similar. 3'') I didn't find, on the mri_glmfit help page, how masks can be formed out of one of the atlas structures, e.g. lh_S_intrapariet_and_P_trans ... The --table argument is also not present anywhere on that page.. You can run mri_annotation2label to convert an annotation to label, then pass the label to glmfit. 3''') Would it not be a/parc/stats2table rather than a/seg/stats2table, if the ROI in question was cortical and not subcortical? Is the difference between what FS calls segmentation and parcellation just terminology, i.e. the former delineates subcortical structures and the latter delineates cortical structures? Or does it imply anything else? Whether you use one or the other depends on whether you generate the individual table with mris_anatomical_stats (aparcstats2table) or mri_segstats (asegstats2table) 4) How do the results of these two different types of ROI group analyses differ, and is one of them more correct than the other: A) running the command prompt version of QDEC within the confines of a certain atlas-defined ROI, and looking at the resulting statistical map (clusters), as per question 3; B) extracting the CT values for that ROI for all subjects using aparcstats2table, and doing t-tests to look for a group difference. Oops, looks like these are the two I mentioned from #3 above. The first is an exploratory analysis in which the groups are compared on a vertex-by-vertex basis. If there is a subset of vertices that are different between the groups, it may show up in the exploratory analysis. However, the effect may be small at each vertex and averaging over the vertices may improve your power (unless the effect is only at a few vertices). One is not more correct than the other, just testing different hypotheses. 4') Can the second option (averaging the CT values within the ROI) not also be done by taking the values from the table into SPSS and simply doing an independent samples t-test? Is that not equivalent to what mri_glmfit would do in this case? Yes, it should be the same. And one more question: 5) Can the statistical map in QDEC be built using a lower, uncorrected p value (e.g. 0.0001) instead of an FDR-corrected test value? Yes, just set the threshold (FDR is off by default). doug Thanks!! Tudor doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Re: [Freesurfer] segfault during rfx with mri_glmfit
Hi Alex, is it actually running out of memory? Otherwise, nothing comes to mind. If you tar up all the inputs and drop them at our file drop I'll take a look. doug On 05/07/2013 10:24 AM, Alex Kell wrote: hi freesurfers, i am running into a segfault whenever i try to use mri_glmfit to run a random effects analysis. (this is in the volume, not on the surface.) here's my call: mri_glmfit \ --y $ces_fpath \ --X $design_mat_fpath \ --C $c1_fpath \ --C $c2_fpath \ --C $c3_fpath \ --mask $mask_fpath \ --glmdir $glmdir_fpath \ --nii.gz i've tried a number of things to reduce the memory footprint of the call: -- originally i was using WLS, but i was worried about the memory demands of the cesvar, so i switched to OLS -- i introduced a GM mask -- i downsampled the ces and cesvar images (from 1 mm isotropic [cvs space] to 2 mm isotropic) any thoughts on what could be going wrong here? thanks, guys! alex ps. below are my build stamp, my info dump from mri_glmfit, and an example stderr stdout. my fs build stamp: freesurfer-Linux-centos4_x86_64-dev-20120104 the all info dump from mri_glmfit: ProgramName: mri_glmfit ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2013/05/07-14:15:28-GMT BuildTimeStamp: Jan 4 2012 05:11:02 CVS: $Id: mri_glmfit.c,v 1.209 2011/12/16 19:02:28 greve Exp $ User: alexkell Machine: ba7 Platform: Linux PlatformVersion: 2.6.38-16-generic CompilerName: GCC CompilerVersion: 30400 an example stderr and stdout: $Id: mri_glmfit.c,v 1.209 2011/12/16 19:02:28 greve Exp $ cwd /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_output/F-O cmdline mri_glmfit --y /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz --wls /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.cesvar.F-O.runs_1234.2x2x2.nii.gz --X /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//design_matrix.dat --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//asd.mtx --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//tc.mtx --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//tc-asd.mtx --mask /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input/cvs.gmMask.2x2x2.nii.gz --glmdir /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O --yhat-save --eres-save --save-cond --nii.gz sysname Linux hostname ba7 machine x86_64 user alexkell FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_input/cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz logyflag 0 X /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//design_matrix.dat usedti 0 mask /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input/cvs.gmMask.2x2x2.nii.gz maskinv 0 glmdir /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O IllCondOK 0 ReScaleX 1 DoFFx 0 wFile /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.cesvar.F-O.runs_1234.2x2x2.nii.gz weightinv 1 weightsqrt 1 Creating output directory /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O Loading y from /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_input/cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz Saving design matrix to /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O/Xg.dat Normalized matrix condition is 1 Matrix condition is 2.21429 Pruning voxels by thr: 0.00 Found 115353 voxels in mask Saving mask to /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O/mask.nii.gz search space = 922824.00 Segmentation fault ___ 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.
Re: [Freesurfer] Probably activation due to vessels
When you use -per-session, it uses the first image of the first run as the template. All runs are motion-corrected to this template, and the template is registered to the anatomical. In this way, all images get aligned to the anatomical. The -per-session command means that there is only one template and so only one register.dof6.dat. If you want one for each run you would use -per-run. doug On 05/07/2013 10:51 AM, Jörg Pfannmöller wrote: Hi, the problem is that there is only one register.dof6.dat in the bold folder. I expected a register.dof6.dat in each run folder. I did not see an error message, but have attached a log file to this mail. A solution of this problem would help me to simplify my workflow and improve the analysis. Thanks in advance. Joerg On Mon, 06 May 2013 10:48:14 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: If you use -per-session, all of them should be processed. Why do you think they are not? Also, just saying something is not working is not very informative. Send command lines and terminal output of the error. thanks! doug On 05/06/2013 05:46 AM, Jörg Pfannmöller wrote: Sorry, I have to cancel my last contribution. Another Problem crossed my way. If I have more than one run, only the first one is preprocessed if i use -per-session. What can I do about it? If I use -per-run all runs are preprocessed, but selxavg3-sess tells me that it can not determine the file format of the fmc files. Actually those files are called fmcpr, if I use -per-run. How can do I have to proceed if there is more than one run? On Mon, 6 May 2013 10:54:54 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Thanks for your help. It works fine if one uses preproc-sess -per-run -fwhm 5 -fsd bold -s sess01 ... . On Fri, 19 Oct 2012 12:49:00 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to run preproc like: preproc-sess -per-session -fwhm 5 -fsd bold -s sess01 In this case, you are just specifiying -per-session and not specifying -mni305 or -surface When you run mkanalysis-sess, specify -native instead of -mni305 or -surface, like: mkanalysis-sess -native -fwhm 5 ... doug On 10/19/2012 03:59 AM, Jörg Pfannmöller wrote: Hi Doug, the preprocessing is fine the quaility factor for the registration between functional and anatomical is ~0.3. Have I to use feat to do the volume analysis? Cheers pfannmoe On Thu, 18 Oct 2012 11:50:38 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: It is too hard to tell what is going on here from just this image. I would not immediately conclude that it is a vessel. Does the activation otherwise look ok? What about other contrasts? Is the registration accurate? When trying to debug these things, it often makes sense to analyze the data in the volume. doug On 10/17/2012 12:31 PM, Jörg Pfannmöller wrote: It is attached to this mail. On Tue, 16 Oct 2012 16:16:54 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: can you send a pic? On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote: Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns.
Re: [Freesurfer] Using FSL matrix for Talairach transform
Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure what regdat2xfm is doing. doug On 05/07/2013 12:42 PM, Johannes Klein wrote: Dear all, I have some tricky subjects that I cannot get to register properly with the standard Talairach process, or even the use-mritotal option. However, with some fiddling, I've produced a reasonable registration matrix with FSL's FLIRT. I'm now looking to convert my FSL registration matrix, and use it as Freesurfer's Talairach transform. From the documentation, I gathered that I need to get it into Freesurfer's xfm format, and I suppose this is a two step process. I converted the FLIRT-provided matrix cor2raw.xfm like so: tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat I then converted register.dat to the xfm data format: regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz register.dat tal.xfm and finally replaced talairach.xfm in the transforms directory with the output of the last command. Unfortunately, this doesn't work, and the transform is very much off target when I view it in tkregister2. Obviously, I've made a mistake when converting between the different transforms - could anybody point me in the right direction? Thanks all, Johannes ___ 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.
[Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?
Dear Freesurfer gurus, At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command? Thanks very much for your insight -- and I enjoyed the course! /Katie Surrence -- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute ___ 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] using T2* weighted scans to assist with dura stripping in a GE scanner?
Hi Katie I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain. cheers Bruce On Tue, 7 May 2013, Katie Surrence wrote: Dear Freesurfer gurus, At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command? Thanks very much for your insight -- and I enjoyed the course! /Katie Surrence -- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute ___ 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] segfault during rfx with mri_glmfit
hi doug, thanks for the quick response. i got it to work -- apparently the 5.1.x developmental version i was using had some problem in mri_glmfit. when i switched to the stable 5.1 version (build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0) it ran perfectly smoothly. unfortunately, i'm not sure how useful it would be to others on this listserv. :-) alex On Tue, May 7, 2013 at 2:06 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Alex, is it actually running out of memory? Otherwise, nothing comes to mind. If you tar up all the inputs and drop them at our file drop I'll take a look. doug On 05/07/2013 10:24 AM, Alex Kell wrote: hi freesurfers, i am running into a segfault whenever i try to use mri_glmfit to run a random effects analysis. (this is in the volume, not on the surface.) here's my call: mri_glmfit \ --y $ces_fpath \ --X $design_mat_fpath \ --C $c1_fpath \ --C $c2_fpath \ --C $c3_fpath \ --mask $mask_fpath \ --glmdir $glmdir_fpath \ --nii.gz i've tried a number of things to reduce the memory footprint of the call: -- originally i was using WLS, but i was worried about the memory demands of the cesvar, so i switched to OLS -- i introduced a GM mask -- i downsampled the ces and cesvar images (from 1 mm isotropic [cvs space] to 2 mm isotropic) any thoughts on what could be going wrong here? thanks, guys! alex ps. below are my build stamp, my info dump from mri_glmfit, and an example stderr stdout. my fs build stamp: freesurfer-Linux-centos4_x86_64-dev-20120104 the all info dump from mri_glmfit: ProgramName: mri_glmfit ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2013/05/07-14:15:28-GMT BuildTimeStamp: Jan 4 2012 05:11:02 CVS: $Id: mri_glmfit.c,v 1.209 2011/12/16 19:02:28 greve Exp $ User: alexkell Machine: ba7 Platform: Linux PlatformVersion: 2.6.38-16-generic CompilerName: GCC CompilerVersion: 30400 an example stderr and stdout: $Id: mri_glmfit.c,v 1.209 2011/12/16 19:02:28 greve Exp $ cwd /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_output/F-O cmdline mri_glmfit --y /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz --wls /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.cesvar.F-O.runs_1234.2x2x2.nii.gz --X /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//design_matrix.dat --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//asd.mtx --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//tc.mtx --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//tc-asd.mtx --mask /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input/cvs.gmMask.2x2x2.nii.gz --glmdir /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O --yhat-save --eres-save --save-cond --nii.gz sysname Linux hostname ba7 machine x86_64 user alexkell FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_input/cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz logyflag 0 X /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//design_matrix.dat usedti 0 mask /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input/cvs.gmMask.2x2x2.nii.gz maskinv 0 glmdir /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O IllCondOK 0 ReScaleX 1 DoFFx 0 wFile /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.cesvar.F-O.runs_1234.2x2x2.nii.gz weightinv 1 weightsqrt 1 Creating output directory /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O Loading y from /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_input/cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz Saving design matrix to /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O/Xg.dat Normalized matrix condition is 1 Matrix condition is 2.21429 Pruning voxels by thr: 0.00 Found 115353 voxels in mask Saving mask to /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O/mask.nii.gz search space = 922824.00 Segmentation fault ___ 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
Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
Hi Nick, It complains about libtix8.1.8.4.so missing. I add $FREESURFER_HOME/lib/tcltktixblt/lib/ to the LD_LIBRARY_PATH variable, but it still complains about the license and does not open bert. Tried the dev build and 5.3 beta, which also fail at the license. Why not remove the requirement and have people agree to a license prior to downloading? Lots of folks probably enter bogus information into the registration form anyway. Just trying to be constructive. Thanks very much for your help Nick On 05/07/2013 12:14 PM, Nick Schmansky wrote: Nicola and Nick, Can you try the tkmedit.bin found here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ copy it to the freesurfer/tktools directory (the wrapper script 'tkmedit' in the bin dir calls the binary in the tktools dir). I'm hoping the problem you are seeing is the same one that others have seen on Fedora 19 and Ubuntu 13 which is fixed for the upcoming 5.3 release. Nick On Tue, 2013-05-07 at 12:15 -0400, Nicola Toschi wrote: Hi Nick, hi List, I have been having the exact same problem (also posted it on this list) with every freesurfer version on Opensuse 12.3, and haven't been able to sort it out. Any luck with it? Any pointers would be highly appreciated. Thanks in advance, Nicola On 5/1/2013 4:42 PM, Nick Jones wrote: Hi, I've run into a license problem with the latest version of Freesurfer on OpenSuse 12.3. 64 bit. FREESURFER_HOME: /usr/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Kernel info: Linux 3.7.10-1.1-desktop x86_64 When running a test: /usr/freesurferecho $shell /bin/tcsh /usr/freesurfersource SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/freesurfer FSFAST_HOME /usr/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/freesurfer/subjects MNI_DIR /usr/freesurfer/mni FSL_DIR /usr/fsl /usr/freesurfertkmedit bert orig.mgz -- ERROR: Invalid FreeSurfer license key found in license file /usr/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- /usr/freesurfercat .license hotm...@hotmail.com 14743 *C5.JPynIz8mt /usr/freesurfer This license file has been obfuscated. /usr/freesurferll -a .license -rw-r--r-- 1 root root 46 Apr 29 09:38 .license /usr/freesurfercat VERSION freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 /usr/freesurferzypper targetos openSUSE-12.3-x86_64 /usr/freesurferuname -a Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC 2013 (82d3f21) x86_64 x86_64 x86_64 GNU/Linux Name: tcl Version: 8.5.12-3.1.3 Name: tk Version: 8.5.12-3.1.1 Thanks to anyone who can provide some insight or workaround. I'm also curious if anyone knows the reasoning behind using this type of license mechanism, as opposed to agreeing to a license prior to downloading, like FSL or 3DSlicer? Nick ___ 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 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
Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?
Hi Bruce, Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation? Cheers, Souheil - Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.in...@nih.govmailto:souheil.in...@nih.gov On May 7, 2013, at 2:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Katie I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain. cheers Bruce On Tue, 7 May 2013, Katie Surrence wrote: Dear Freesurfer gurus, At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command? Thanks very much for your insight -- and I enjoyed the course! /Katie Surrence -- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?
no, of course not :) On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote: Hi Bruce, Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation? Cheers, Souheil - Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.in...@nih.govmailto:souheil.in...@nih.gov On May 7, 2013, at 2:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Katie I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain. cheers Bruce On Tue, 7 May 2013, Katie Surrence wrote: Dear Freesurfer gurus, At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command? Thanks very much for your insight -- and I enjoyed the course! /Katie Surrence -- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 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] using T2* weighted scans to assist with dura stripping in a GE scanner?
thanks :-) On May 7, 2013, at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, of course not :) On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote: Hi Bruce, Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation? Cheers, Souheil - Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.in...@nih.govmailto:souheil.in...@nih.gov On May 7, 2013, at 2:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Katie I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain. cheers Bruce On Tue, 7 May 2013, Katie Surrence wrote: Dear Freesurfer gurus, At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command? Thanks very much for your insight -- and I enjoyed the course! /Katie Surrence -- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Qdec and GLM ROI analysis
I am interested ing doing a group surfaces analysis like that specified in: ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis, or http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=%28cortical%29%7C%28thickness%29 but I want to limit the analysis to a specific ROI. how do i do this? -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ 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] using T2* weighted scans to assist with dura stripping in a GE scanner?
actually Matt Glasser points out that a brief description is in his paper that is coming out soon, and there is also some description in Andre's multi-echo mprage paper Bruce On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote: thanks :-) On May 7, 2013, at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, of course not :) On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote: Hi Bruce, Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation? Cheers, Souheil - Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.in...@nih.govmailto:souheil.in...@nih.gov On May 7, 2013, at 2:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Katie I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain. cheers Bruce On Tue, 7 May 2013, Katie Surrence wrote: Dear Freesurfer gurus, At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command? Thanks very much for your insight -- and I enjoyed the course! /Katie Surrence -- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 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] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
Hi Nick, sorry - I should have been more specific. I get the same error with *any* FS command or script (recon-all, mri_glmfit), so in effect ever since the upgrade I am not able to use FS at all. The tkmedit patch you posted is only missing a library on my system though, which I can fix - so maybe that's a pointer towards the root of the problem? Thanks again, Nicola On 5/7/2013 2:57 PM, Nick Jones wrote: Hi Nick, It complains about libtix8.1.8.4.so missing. I add $FREESURFER_HOME/lib/tcltktixblt/lib/ to the LD_LIBRARY_PATH variable, but it still complains about the license and does not open bert. Tried the dev build and 5.3 beta, which also fail at the license. Why not remove the requirement and have people agree to a license prior to downloading? Lots of folks probably enter bogus information into the registration form anyway. Just trying to be constructive. Thanks very much for your help Nick On 05/07/2013 12:14 PM, Nick Schmansky wrote: Nicola and Nick, Can you try the tkmedit.bin found here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ copy it to the freesurfer/tktools directory (the wrapper script 'tkmedit' in the bin dir calls the binary in the tktools dir). I'm hoping the problem you are seeing is the same one that others have seen on Fedora 19 and Ubuntu 13 which is fixed for the upcoming 5.3 release. Nick On Tue, 2013-05-07 at 12:15 -0400, Nicola Toschi wrote: Hi Nick, hi List, I have been having the exact same problem (also posted it on this list) with every freesurfer version on Opensuse 12.3, and haven't been able to sort it out. Any luck with it? Any pointers would be highly appreciated. Thanks in advance, Nicola On 5/1/2013 4:42 PM, Nick Jones wrote: Hi, I've run into a license problem with the latest version of Freesurfer on OpenSuse 12.3. 64 bit. FREESURFER_HOME: /usr/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Kernel info: Linux 3.7.10-1.1-desktop x86_64 When running a test: /usr/freesurferecho $shell /bin/tcsh /usr/freesurfersource SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/freesurfer FSFAST_HOME /usr/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/freesurfer/subjects MNI_DIR /usr/freesurfer/mni FSL_DIR /usr/fsl /usr/freesurfertkmedit bert orig.mgz -- ERROR: Invalid FreeSurfer license key found in license file /usr/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- /usr/freesurfercat .license hotm...@hotmail.com 14743 *C5.JPynIz8mt /usr/freesurfer This license file has been obfuscated. /usr/freesurferll -a .license -rw-r--r-- 1 root root 46 Apr 29 09:38 .license /usr/freesurfercat VERSION freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 /usr/freesurferzypper targetos openSUSE-12.3-x86_64 /usr/freesurferuname -a Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC 2013 (82d3f21) x86_64 x86_64 x86_64 GNU/Linux Name: tcl Version: 8.5.12-3.1.3 Name: tk Version: 8.5.12-3.1.1 Thanks to anyone who can provide some insight or workaround. I'm also curious if anyone knows the reasoning behind using this type of license mechanism, as opposed to agreeing to a license prior to downloading, like FSL or 3DSlicer? Nick ___ 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 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
[Freesurfer] Freesurfer segmntation for ICBM or Colin27
Hello FreeSurferusers, Has anyone processed ICBM or Colin27 template through Freesurfer V5.0.0 (or higher) or does anyone know if such data is available in public database? Thank you. Priyanka Bhatt ___ 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 segmntation for ICBM or Colin27
Hi Priyanka, You can download it from the Surfrend web page and then recon-all it with the version you want (don`t use the -i, just the -s with the subject name you choose). Regards, Gari On May 7, 2013 10:56 PM, Priyanka bme.priya...@gmail.com wrote: Hello FreeSurferusers, Has anyone processed ICBM or Colin27 template through Freesurfer V5.0.0 (or higher) or does anyone know if such data is available in public database? Thank you. Priyanka Bhatt ___ 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 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] Google Talk 使用邀请
--- yufeng huang邀请您使用 Google Talk。 如果您已经拥有 Google 帐户，请登录 Gmail 并接受此聊天邀请： http://mail.google.com/mail/b-60fdfa524c-703f0dba08-8eKfT6qRXAGCd7RaLzjh4b7UCP0 要注册 Google 帐户并开始使用 Google Talk，您可以访问： http://mail.google.com/mail/a-60fdfa524c-703f0dba08-8eKfT6qRXAGCd7RaLzjh4b7UCP0?pc=zh_cn-rf---a 要了解详情，请访问： http://www.google.com/intl/zh-CN/landing/accounts/ 此致， Google 小组敬上 ___ 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.
