Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

Re: [Freesurfer] Permission denied mri_surf2surf
by fsbuild 09 Sep '20

09 Sep '20

External Email - Use Caution Hello Ellen, I suspect that you really do not have the system privileges to read/write every subject directory.  I have run into this with other commands that scan multiple subject directories. Assuming there is one top level directory that contains all the subject directories, and it’s OK for you to try and set/change permissions on those files, then in terminal window you could “cd” to that parent directory, $ cd <path to top of tree containing all subject subdirectories> - and then try running the following command, $ find . -maxdepth 1 -type d -exec chmod 755 {} \; -print That will try and change the permissions of every subdirectory there such that you can read and write to it.  But if you don’t have permission to access some of those directories, then you will get an error..  You may have to find someone wit, e.g., admin/root. privileges to change the permissions on the subdirectories the chmod command fails on. - R. On Sep 9, 2020, at 03:19, Ellen Ji <ellen.ji(a)bli.uzh.ch> wrote:       External Email - Use Caution        Dear experts,I created a loop for mri_surf2surf so that it would run for 300+ subjects. For most of them, it ran successfully. However, it did not work for 30 subjects. I then went to investigate one by one and I am getting a Permission denied error for some reason. I confirm that recon-all has been performed and also that I have read/write/execute permissions. See below for the log. Any ideas why this could be happening to specific subjects?            mri_surf2surf \                --srcsubject fsaverage_sym \                --trgsubject SPN01_CMH_0079_01 \                --hemi lh \                --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot \                --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annotSetting mapmethod to nnf7.1.0setenv SUBJECTS_DIR /home/eji/projects/spins/preproc/freesurfer/subjects/w0cd /home/eji/projects/spins/preproc/freesurfer/subjects/w0mri_surf2surf --srcsubject fsaverage_sym --trgsubject SPN01_CMH_0079_01 --hemi lh --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annotsysname  Linuxhostname nu2machine  x86_64user     ejisrcsubject = fsaverage_symsrcval     = (null)srctype    =trgsubject = SPN01_CMH_0079_01trgval     = SPN01_CMH_0079_01/label/lh.500_sym.aparc.annottrgtype    =srcsurfreg = sphere.regtrgsurfreg = sphere.regsrchemi    = lhtrghemi    = lhframe      = 0fwhm-in    = 0fwhm-out   = 0label-src  = (null)label-trg  = (null)OKToRevFaceOrder  = 1UseDualHemi = 0Reading source surface reg /home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.sphere.regLoading source dataReading surface file /home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.origreading colortable from annotation file...colortable with 161 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)Reading target surface reg /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0079_01/surf/lh.sphere.regDoneUsing surf2surf_nnfr()Mapping Source Volume onto Source Subject Surfacesurf2surf_nnfr: building source hash (res=16).Surf2Surf: Forward Loop (123600)Surf2Surf: Dividing by number of hits (123600)INFO: nSrcLost = 61776nTrg121 = 123600, nTrgMulti =     0, MnTrgMultiHits = 0nSrc121 = 85136, nSrcLost = 61776, nSrcMulti = 78706, MnSrcMultiHits = 0.488705Saving target dataConverting to target annotSaving to target annot SPN01_CMH_0079_01/label/lh.500_sym.aparc.annoterror: Permission deniederror: could not write annot file SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Permission denied mri_surf2surf
by Ellen Ji 09 Sep '20

09 Sep '20

External Email - Use Caution Dear experts, I created a loop for mri_surf2surf so that it would run for 300+ subjects. For most of them, it ran successfully. However, it did not work for 30 subjects. I then went to investigate one by one and I am getting a Permission denied error for some reason. I confirm that recon-all has been performed and also that I have read/write/execute permissions. See below for the log. Any ideas why this could be happening to specific subjects? mri_surf2surf \ --srcsubject fsaverage_sym \ --trgsubject SPN01_CMH_0079_01 \ --hemi lh \ --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot \ --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot Setting mapmethod to nnf 7.1.0 setenv SUBJECTS_DIR /home/eji/projects/spins/preproc/freesurfer/subjects/w0 cd /home/eji/projects/spins/preproc/freesurfer/subjects/w0 mri_surf2surf --srcsubject fsaverage_sym --trgsubject SPN01_CMH_0079_01 --hemi lh --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot sysname Linux hostname nu2 machine x86_64 user eji srcsubject = fsaverage_sym srcval = (null) srctype = trgsubject = SPN01_CMH_0079_01 trgval = SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.sphere.reg Loading source data Reading surface file /home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.orig reading colortable from annotation file... colortable with 161 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) Reading target surface reg /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0079_01/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (123600) Surf2Surf: Dividing by number of hits (123600) INFO: nSrcLost = 61776 nTrg121 = 123600, nTrgMulti = 0, MnTrgMultiHits = 0 nSrc121 = 85136, nSrcLost = 61776, nSrcMulti = 78706, MnSrcMultiHits = 0.488705 Saving target data Converting to target annot Saving to target annot SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot error: Permission denied error: could not write annot file SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot

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Re: [Freesurfer] interpreting file (cache.th13.abs.y.ocn.dat) from longitudinal vertex-wise analysis
by Rizvi, Batool 08 Sep '20

08 Sep '20

External Email - Use Caution Thanks for the info, Dr. Greve! So for the files I used for the --y argument were stacked files of this file: lh.long.thickness-spc.fwhm10.fsaverage.mgh or rh.long.thickness-spc.fwhm10.fsaverage.mgh. So would my interpretation of the ocn.dat file be that each value is the symmetrized percent change in thickness of the significant cluster for each subject? Thanks again, Batool

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Re: [Freesurfer] G_subcallosal region is missing
by Marina Fernández 08 Sep '20

08 Sep '20

External Email - Use Caution Hi Doug, I sent you the images attached to the email and also through FTP File Exchange. Thank you for your attention. Best regards, Marina > ____________________________________________ > Douglas N. Greve > I'm still not understanding what is happening. Can you send three pics of > the inflated surface of same location, one with cortex.label, one with > aparc.annot, and one with aparc.a2009s.annot? Also, please remember to > include previous emails so that I have context, thanks > > On 9/3/2020 9:55 AM, Marina Fernández wrote: External Email - Use Caution Sorry for the misunderstanding Doug . I have checked the lh.aparc.annot on the surface and there is no G_subcallosal label in these subjects. In that region are the G_and_S_cingul-Ant label / S_pericallosal labels. On the other hand, the surface appears normal. What do you recommend us to do? Thank you in advance. Marina. Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Wed, 02 Sep 2020 10:31:13 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Sorry, I meant to look on the surface and see if the label is there and what the lh.aparc.annot looks like there On 9/2/2020 11:05 AM, Marina Fernández wrote: External Email - Use Caution Hi Doug, When I load the volume aparc.a2009s+aseg.mgz in a subject without the G_subcallosal region in the lh.aparc.a2009s.stats file, I can see that in the other hemisphere (right in this case) there is G_subcallosal while in the left hemisphere this contralateral region is filled by the lh_S_suborbital region. So, it's covered by another label. What should we do? Best wishes, Marina ---------------------------------------------------------------------------------------------------------------------------- Douglas N. Greve < https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from… > Wed, 02 Sep 2020 07:23:58 -0700 < https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date… > Does the cortex label cover it? What does the aparc look like in that area? On 9/2/2020 6:09 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I have noticed that some subjects don't show the G_subcallosal region in the *h.aparc.a2009s.stats file. Do you know why is this happening? Is there a way to fix it? Thank you in advance. Best regards, Marina _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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BrainSegNotVent
by Harkey, Thomas Jarrott 08 Sep '20

08 Sep '20

External Email - Use Caution Hello, I am a student learning free surfer. I was able to obtain intracranial volume by running recon-all –i file.dcm –subject bert –autorecon1 and then mri_segstats --subject bert --etiv-only How can I obtain the BrainSegNotVent volume? I have tried mri_segstats --subject bert --brain-vol-from-seg however, “ERROR: must specify a segmentation volume” Can this be calculated using the data from autorecon1, or do I need to run -all? Which segmentation do I need to specify? My contact information is below, Thank you! -- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 TJHarkey(a)uams.edu<mailto:TJHarkey@uams.edu> ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Re: [Freesurfer] lobe annotation and stats file
by Marina Fernández 08 Sep '20

08 Sep '20

External Email - Use Caution Hi Doug, I used the command that you sent me but I have the same error message (ERROR: stating file /usr/local/freesurfer/...). Do you know other options? Thank you in advance. Marina ----------------------------------------------------- Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Tue, 08 Sep 2020 08:14:19 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Try something like this mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobe.stats -b -a ../label/lh.lobe.annot fsm010 lh white On 9/8/2020 7:58 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I would like to get a .stats file this the volume and thickness of lobe annotation, so I am following the steps indicated in this link https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. Specifically, I used these commands: mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a s_001/label/lh.lobe.annot -f s_001/stats/lh.lobe.stats -b s_001 lh The output file that I get (lh.lobe.stats) seems normal and contains the measurements that I need (volume and thickness). The problem is that the terminal output contains this error message: ERROR: stating file /usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot (below you can find the full terminal output) What I have to do to obtain the lh.lobe.stats file (with the same or similar stucture) without the error message? Best regards, Marina % /TERMINAL OUTPUT / % / subject = s_001 annotation = aparc hemi = rh surface = white Reading surface /usr/local/freesurfer/subjects/s_001/surf/rh.white Loading annotations from /usr/local/freesurfer/subjects/s_001/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 MRISmergeAnnotations: parcCount=11, newparcname=frontal mri_annotation2 supposed to be reproducible but seed not set MRISmergeAnnotations: parcCount=9, newparcname=temporal MRISmergeAnnotations: parcCount=5, newparcname=parietal MRISmergeAnnotations: parcCount=4, newparcname=occipital MRISmergeAnnotations: parcCount=4, newparcname=cingulate computing statistics for each annotation in s_001/label/rh.lobe.annot. reading volume /usr/local/freesurfer/subjects/s_001/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/s_001/surf/rh.white... Using TH3 vertex volume calc Total face volume 176610 Total vertex volume 173305 (mask=0) reading input pial surface /usr/local/freesurfer/subjects/s_001/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/s_001/surf/rh.white... reading colortable from annotation file... colortable with 8 entries read (originally none) table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name ERROR: stating file /usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot atlas_icv (eTIV) = 1198953 mm^3 (det: 1.624839 ) 37262 24668 63218 2.363 0.474 0.124 0.029 414 43.8 frontal 3602 2412 6370 2.374 0.615 0.137 0.027 54 3.8 cingulate 12917 8443 18251 2.024 0.428 0.134 0.030 171 15.6 occipital 19235 12890 36112 2.488 0.535 0.119 0.028 211 21.0 temporal 26568 17417 41499 2.204 0.466 0.119 0.024 287 25.6 parietal 2510 1617 4741 3.018 0.820 0.126 0.036 28 3.9 insula/ _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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interpreting file (cache.th13.abs.y.ocn.dat) from longitudinal vertex-wise analysis
by Rizvi, Batool 08 Sep '20

08 Sep '20

External Email - Use Caution Hi FreeSurfer team, After running longitudinal FS, and running mri_glmfit using files that measured spc, we found clusters associated with our continuous variable (WMH volume) after controlling for other covariates. I was wondering though, do the values found in cache.th13.abs.y.ocn.dat reflect the change in thickness (as measured by spc) for each subject of the cluster found to be significantly associated? I read other posts that it was a value of thickness of each cluster, but I wasn't sure if the same was true for a longitudinal analysis (spc), as the file contains both positive and negative numbers. Thanks so much for your help! Batool

2 1

freeview Inflated image with mosaic
by Wei Shao 08 Sep '20

08 Sep '20

External Email - Use Caution Hi, Freesurfer Team My name is Wei Shao, as you can see, whenever I tried to Freeview Inflated image , it gives me the picture with mosaic. I was wondering this is because of hardware or the setting? Thanks Best, Wei [image: 3D freesurfer.PNG]

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lobe annotation and stats file
by Marina Fernández 08 Sep '20

08 Sep '20

External Email - Use Caution Dear experts, I would like to get a .stats file this the volume and thickness of lobe annotation, so I am following the steps indicated in this link https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. Specifically, I used these commands: mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a s_001/label/lh.lobe.annot -f s_001/stats/lh.lobe.stats -b s_001 lh The output file that I get (lh.lobe.stats) seems normal and contains the measurements that I need (volume and thickness). The problem is that the terminal output contains this error message: ERROR: stating file /usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot (below you can find the full terminal output) What I have to do to obtain the lh.lobe.stats file (with the same or similar stucture) without the error message? Best regards, Marina % *TERMINAL OUTPUT * % *subject = s_001annotation = aparchemi = rhsurface = whiteReading surface /usr/local/freesurfer/subjects/s_001/surf/rh.whiteLoading annotations from /usr/local/freesurfer/subjects/s_001/label/rh.aparc.annotreading colortable from annotation file...colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)Seg base 2000MRISmergeAnnotations: parcCount=11, newparcname=frontalmri_annotation2 supposed to be reproducible but seed not setMRISmergeAnnotations: parcCount=9, newparcname=temporalMRISmergeAnnotations: parcCount=5, newparcname=parietalMRISmergeAnnotations: parcCount=4, newparcname=occipitalMRISmergeAnnotations: parcCount=4, newparcname=cingulatecomputing statistics for each annotation in s_001/label/rh.lobe.annot.reading volume /usr/local/freesurfer/subjects/s_001/mri/wm.mgz...reading input surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...Using TH3 vertex volume calcTotal face volume 176610Total vertex volume 173305 (mask=0)reading input pial surface /usr/local/freesurfer/subjects/s_001/surf/rh.pial...reading input white surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...reading colortable from annotation file...colortable with 8 entries read (originally none)table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure nameERROR: stating file /usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annotatlas_icv (eTIV) = 1198953 mm^3 (det: 1.624839 )37262 24668 63218 2.363 0.474 0.124 0.029 414 43.8 frontal 3602 2412 6370 2.374 0.615 0.137 0.027 54 3.8 cingulate12917 8443 18251 2.024 0.428 0.134 0.030 171 15.6 occipital19235 12890 36112 2.488 0.535 0.119 0.028 211 21.0 temporal26568 17417 41499 2.204 0.466 0.119 0.024 287 25.6 parietal 2510 1617 4741 3.018 0.820 0.126 0.036 28 3.9 insula*

2 1

mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999
by Paul 08 Sep '20

08 Sep '20

2 1

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Freesurfer September 2020