Freesurfer

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30132 discussions

qdec question
by Giovanni de Marco 31 Dec '17

31 Dec '17

Hello, I’ve got a question concerning qdec running with freesurfer. I just downloaded the latest version of freesurfer. Before to run qdec, I read than I have to run "recon-all -s ID -all" (about 7 hours) and then recon-all -s ID -qcache (about 5'). So I tried it with one subject and everything is fine. Indeed, I got the files like *.fwhm5.fsaverage.mgh, *.fwhm10.fsaverage.mgh, *.fwhm20.fsaverage.mgh, etc... in the surf folder absolutely necessary for qdec. My question is very simple : I have already treated all my subjects (n = 45) two years ago. Today, I would like to use qdec. Do I need to restart *for each subject* all my preprocessing with recon-all -s ID -all followed by recon-all -s ID -qcache ? or Is there a routine faster to get the smoothed surfaces for each subject ? Many thank for any advice. Best wishes and happy new year. Giovanni

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Re: [Freesurfer] FreeSurfer recon-all issue
by Antonin Skoch 31 Dec '17

31 Dec '17

Dear Shadia, please check, that you really edited your recon.all, as I suggested in my previous mail. Your recon-all file is located here: /home/s1163658/freesurferv60/bin/recon-all According to your recon-all.log, there is still an ln -s command invoked (which should be replaced by cp command). It is normal that the log from new invocation of recon-all is appended to current recon-all.log. As a test, you can try to run only the step which is currently failing: recon-all -s your_subject -curvHK Also, by default, recon-all invocation does not automatically account already finished steps. To skip already successfully finished steps, you can try to run recon-all -s your_subject -make all (not sure if it works OK in v6) or explicitly list steps which need to be run: recon-all -s your_subject -curvHK -curvstats -autorecon3 Antonin Dear Antonin, Thank you for your suggestions at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055319.… . I've tried both, but the process still fails at the same point. It appears that I now am left with a recon-all log file (attached) that is double in length (run 1 ending at line 4187, and run 2 ending at 8276), both of which have started from step 1, rather than run 2 resuming from where we last stopped. Should I be adding certain flags for recon-all to resume rather than start from the beginning? The way I did it was the same as before, but without the -I flag in the second run, as suggested by the recon-all prompt. Thanks again. Shadia -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -----Original Message----- From: MIKHAEL Shadia Sent: 28 December 2017 10:12 To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: FreeSurfer recon-all issue Hello all, I'm having trouble with recon-all on a Linux server, I'm running into the following error for all of my subjects: ..... mris_curvature -w lh.white.preaparc total integrated curvature = 6.657*4pi (83.654) --> -6 handles ICI = 129.9, FI = 1309.2, variation=20703.115 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: creating symbolic link `lh.white.H': Operation not supported Linux bsrv10 ..... #1 SMP Tue Nov 15 14:13:21 CST 2016 x86_64 x86_64 x86_64 GNU/Linux I've tried to create a symbolic link as suggested in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/04047… , but I still get a message saying operation not supported ln -s /usr/local/freesurfer/subjects/fsaverage /home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia ln: creating symbolic link `/home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia/fsaverage': Operation not supported I've also tried to manually create the symbolic link in that last line: ln -s lh.white.preaparc.H lh.white.H But again it says operation not supported. Recon-all log: attached Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Any advice? Thank you Shadia

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Re: [Freesurfer] FreeSurfer recon-all issue
by MIKHAEL Shadia 31 Dec '17

31 Dec '17

Dear Antonin, Thank you for your suggestions at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055319.… . I've tried both, but the process still fails at the same point. It appears that I now am left with a recon-all log file (attached) that is double in length (run 1 ending at line 4187, and run 2 ending at 8276), both of which have started from step 1, rather than run 2 resuming from where we last stopped. Should I be adding certain flags for recon-all to resume rather than start from the beginning? The way I did it was the same as before, but without the -I flag in the second run, as suggested by the recon-all prompt. Thanks again. Shadia -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -----Original Message----- From: MIKHAEL Shadia Sent: 28 December 2017 10:12 To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: FreeSurfer recon-all issue Hello all, I'm having trouble with recon-all on a Linux server, I'm running into the following error for all of my subjects: ..... mris_curvature -w lh.white.preaparc total integrated curvature = 6.657*4pi (83.654) --> -6 handles ICI = 129.9, FI = 1309.2, variation=20703.115 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: creating symbolic link `lh.white.H': Operation not supported Linux bsrv10 ..... #1 SMP Tue Nov 15 14:13:21 CST 2016 x86_64 x86_64 x86_64 GNU/Linux I've tried to create a symbolic link as suggested in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/04047… , but I still get a message saying operation not supported ln -s /usr/local/freesurfer/subjects/fsaverage /home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia ln: creating symbolic link `/home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia/fsaverage': Operation not supported I've also tried to manually create the symbolic link in that last line: ln -s lh.white.preaparc.H lh.white.H But again it says operation not supported. Recon-all log: attached Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Any advice? Thank you Shadia

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Scan sequences and parameters in hippocampus segmentation.
by Qin weiting 30 Dec '17

30 Dec '17

Dear FreeSurfer experts, I'm sorry that English is not my mother language. I have met some trouble in choosing the scan sequences and parameters of data collecting in hippocampus segmentation, I have read the MORPHOMETRY PROTOCOLS on FreeSurfer Wiki, but our lab only has GE Discovery MR 750W instead of Siemens MRI. How should the T1 and T2 scan sequences and parameters be designed on a GE MR 750W? Thank you very much！ Best, Qin weiting

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skull strip / pial issues on many scans
by Michelle VanTieghem 30 Dec '17

30 Dec '17

Hi Douglas, I am not sure why my previous message (posted Dec 22) did not get posted. I have reported many problems with the skull stripping and resulting issues in freesurfer. To summarize: 1. For our structural scans, we have significant pial matter/dura matter remaining for > 50% of subjects or more (of a dataset of 350 scans). I have tested using freesurfer's gcut and other options, as well as AFNI skull strip, FSL with many options, and even ANTS. 2. We gave up on trying to use surfaces with this dataset, due to the sheer amount of manual intervention that would be needed to edit the brains. A colleague suggested that Freesurfer v 6 may work better than 5.3 , which we had been using. Do you think that would make sense? 3. The aseg almost always labels the remaining skull as gray matter, which then influences the icv and wbv measurements. 4. Recently we have decided to try the longitudinal pipeline. Another problem appears: if a cross-sectional scan does not have any pial matter (as in, it is one of the few that as successfully skull stripped - we call these the "clean" scans) but a template is made from multiple scans from this subject. If one of those other tp scans from this subject has any pial mater remaining, then the (a) the template will include all of the pial matter and (b) the longitudinal version of the "clean" scan now has extra pial matter that gets erroneously labeled as gray matter, or sometimes white matter. I have been trying to solve this for over a year, and I also sent data to freesurfer over the ftp on December 1st using the directions on the freesurfer wiki, if you want to take a look at a single representative scan with this skull strip issue. Thanks! Michelle -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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mri_glmfit-sim and Ftest
by Pauline Duret 29 Dec '17

29 Dec '17

Hi Freesurfer experts! I know we asked this question before, but maybe someone came back from holidays and know the answer! Does Hi Freesurfer experts. Does mri_glmfit-sim Monte-Carlo cluster size correction is also usable for F-test? The doc says that it synthesizes a z map (I assume from a normal distribution) for computing the voxel-wise thresholds and cluster size distribution. Maybe I am wrong with my stats but I wonder if it is ok to use this null-hypothesis to a F-distributed data such as results from a F-test. Thanks! Monte-Carlo cluster size correction is also usable for F-test? (When doing a 3-groups comparison and testing the effect of group on lGI). The doc says that it synthesizes a z map (I assume from a normal distribution) for computing the voxel-wise thresholds and cluster size distribution. Maybe I am wrong with my stats but I wonder if it is ok to use this null-hypothesis to a F-distributed data such as results from a F-test. Thanks so much!

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Re: [Freesurfer] Remove address
by Antonin Skoch 29 Dec '17

29 Dec '17

Dear Antoine, look here: http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Antonin Is it possible to quit the freesurfer mailing list ? Best regards, Antoine

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Question about an error during recon-all process
by 박경일 28 Dec '17

28 Dec '17

Dear experts, I am sorry for asking again. I have some problems in running recon-all. Recon-all process was shut down with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string." I guess this is because of low resolution or small size of images. is it right? Thank you so much for you help in advance. FYI, log file is attached. Kyung

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bbregister error -- Human Connectome Project Data
by Lana Ruck 28 Dec '17

28 Dec '17

Hello, I am currently starting a project with the minimally pre-processed rfMRI from the Human Connectome Project, but I need to do some additional processing first. This includes smoothing at 6mm FWHM and projection onto the fsaverage4 surface. I have smoothed the pre-processed rfMRI data using mri_convert (and have also converted the provided brain-extracted anatomical), but I am having issues registering the smoothed rfMRI volumes, and I understand that I need these register.dat files for mri_vol2surf. I have tried bbregister --init-fsl; bbregister --init-spm; and manual registration using tkregister2. All of them give me the same error--I think it is a path error looking for a subject-specific brain mask (see detailed console errors below). After reading through others' problems with bbregister, I made sure I am running the updated versions of bb- and fsl-register, below: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman bbregister,v 1.75 2016/05/10 20:02:28 greve freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c I also made sure these files had the edits recommended to others, so I don't think this is an previously-addressed issue. That // in all my errors suggests to me that this is a path problem with my HCP data? I am new to FreeSurfer, but I would think that the HCP-pre-determined path organization should be compatible with FSL and FreeSurfer, since their pipelines use both. Is this a compatibility issue with FreeSurfer 6.0? Anyways, I would prefer to use bbregister --init-fsl, but do not know how to point it to the right directory for a brainmask. There is no information provided in any of the --help menus or Wiki pages regarding how to specify brain masks for registration, and the HCP pre-processed data provides multiple 'mask.nii.gz' files that I suppose are not being recognized by bbregister (perhaps because they are not .mgz? I tried converting one to mgz and also got an error from mghWrite). Either way, I have 4 rfMRI runs per subject and over 40 subjects to process, so any advice on this error would be greatly appreciated. Thanks in advance! Lana Ruck Console errors (bolded and underlined) for bbregister --init-fsl, bbregister --init-spm, and tkregister2: [lruck@c5 MNINonLinear]$ bbregister --mov ./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-fsl --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127 Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat.log Wed Dec 27 12:51:51 EST 2017 setenv SUBJECTS_DIR /N/dc2/scratch/lruck/LH_all/ cd /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear /N/soft/rhel6/freesurfer/6.0.0/freesurfer/bin/bbregister --mov ./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-fsl --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux c5.karst.uits.iu.edu 2.6.32-696.16.1.el6.x86_64 #1 SMP Sun Oct 8 09:45:56 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /N/soft/rhel6/freesurfer/6.0.0/freesurfer mri_convert ./Results/rfMRI_REST1_LR/REST1LR.img /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii mri_convert.bin ./Results/rfMRI_REST1_LR/REST1LR.img /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./Results/rfMRI_REST1_LR/REST1LR.img... analyzeRead() roi_scale 0.000000000 TR=720.00, 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 /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii... fslregister --s 101915 --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat --niters 1 --maxangle 90 --tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat.fslregister.log Wed Dec 27 12:51:52 EST 2017 --s 101915 --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat --niters 1 --maxangle 90 --tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov $Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $ c5.karst.uits.iu.edu Linux c5.karst.uits.iu.edu 2.6.32-696.16.1.el6.x86_64 #1 SMP Sun Oct 8 09:45:56 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux nIters 1 *ERROR: cannot find /N/dc2/scratch/lruck/LH_all//101915/mri/brainmask* [lruck@c5 MNINonLinear]$ bbregister --mov ./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-spm --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239 Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat.log Wed Dec 27 12:54:14 EST 2017 setenv SUBJECTS_DIR /N/dc2/scratch/lruck/LH_all/ cd /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear /N/soft/rhel6/freesurfer/6.0.0/freesurfer/bin/bbregister --mov ./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-spm --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux c5.karst.uits.iu.edu 2.6.32-696.16.1.el6.x86_64 #1 SMP Sun Oct 8 09:45:56 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /N/soft/rhel6/freesurfer/6.0.0/freesurfer mri_convert ./Results/rfMRI_REST1_LR/REST1LR.img /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii mri_convert.bin ./Results/rfMRI_REST1_LR/REST1LR.img /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./Results/rfMRI_REST1_LR/REST1LR.img... analyzeRead() roi_scale 0.000000000 TR=720.00, 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 /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii... spmregister --s 101915 --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/reg.init.dat --tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/spmregister Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/spmregister.log Wed Dec 27 12:54:14 EST 2017 --s 101915 --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/reg.init.dat --tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/spmregister $Id: spmregister,v 1.46 2016/02/16 17:17:20 zkaufman Exp $ matlab matlab fmt nii UseSPMGetSpace 1 *ERROR: /N/dc2/scratch/lruck/LH_all//101915/mri/brainmask.mgz not found in either COR or MGZ formats* [lruck@c5 MNINonLinear]$ tkregister2 --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz --regheader --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat --surf tkregister_tcl /N/soft/rhel6/freesurfer/6.0.0/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz reg file /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 *ERROR: could not find orig as either mgz or COR* */N/dc2/scratch/lruck/LH_all//subject-unknown/mri/orig*

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Re: [Freesurfer] FreeSurfer recon-all issue
by Antonin Skoch 28 Dec '17

28 Dec '17

Dear Shadia, There are 2 spots in recon-all where symbolic link is created. The first you can overcome by: find following line in your recon-all: set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix) and replace it by set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix) The second you overcome by copying the directory $FREESURFER_HOME/subjects/fsaverage and all its contents of to your $SUBJECTS_DIR. Then rerun recon-all on your subject. Antonin Skoch Hello all, I'm having trouble with recon-all on a Linux server, I'm running into the following error for all of my subjects: ..... mris_curvature -w lh.white.preaparc total integrated curvature = 6.657*4pi (83.654) --> -6 handles ICI = 129.9, FI = 1309.2, variation=20703.115 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: creating symbolic link `lh.white.H': Operation not supported Linux bsrv10 ..... #1 SMP Tue Nov 15 14:13:21 CST 2016 x86_64 x86_64 x86_64 GNU/Linux I've tried to create a symbolic link as suggested in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/04047… , but I still get a message saying operation not supported ln -s /usr/local/freesurfer/subjects/fsaverage /home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia ln: creating symbolic link `/home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia/fsaverage': Operation not supported I've also tried to manually create the symbolic link in that last line: ln -s lh.white.preaparc.H lh.white.H But again it says operation not supported. Recon-all log: attached Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Any advice? Thank you Shadia

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