[Freesurfer] Error FsFast Tutorial
Hi, I am trying to run the FsFast tutorial, but I am getting the following error: Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study] fernandapalhano% tkmedit-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0 -aparc+aseg tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. ERROR: cannot find /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/register.dof6.dat [Fernanda-Palhanos-Mac-Pro:fsfast/fsfast-tutorial/fb1-analysis-study] fernandapalhano% tksurfer-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0 -hemi lh -aparc tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. tmp: Subscript out of range. $Id: tksurfer-sess,v 1.15.2.1 2010/07/14 16:08:04 greve Exp $ Darwin Fernanda-Palhanos-Mac-Pro.local 10.4.0 Darwin Kernel Version 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 i386 Mon Jan 10 15:08:15 BRT 2011 /Applications/freesurfer/bin/tksurfer list odd-v-0 con/map odd-v-0 /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii maplist /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii mri_concat /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/odd-v-0/sig.nii --o /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/tksconcat.nii ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/sm-gamma-fwhm5/tksconcat.nii ERROR: cannot find /Users/fernandapalhano/Data/fsfast/fsfast-tutorial/fb1-analysis-study/mgh-101.1/bold/register.dof6.dat I checked all the mgh files in fb1-analysis-study and any of them have register.dof6.dat, there is only register.dat. Where can I obtain these file? Thanks in advance, Fernanda Palhano ___ 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] overlay sig.mgh onto T1 vol
Hello, Does anyone knows if is it possible to overlay the surface file sig.mgh onto a T1 vol? I tried the command: tkmedit fsaverage T1.mgz -fthresh 2 -fmax 5 -overlay qdec/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh (where 2 and 5 were the thresholds I used in qdec), but it seems like I have only one point of the sig.mgh (in the slice 128) which is outside the volume. There's another way to do this? Thanks for the help! Fernanda ___ 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] overlay sig.mgh onto T1 vol
Hi Bruce, Thank you for the prompt reply. I tried using mri_surf2vol : mri_surf2vol --surfval qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh --identity fsaverage --template fsaverage/mri/T1.mgz --hemi lh --o teste_sig.mgz gdiagno = -1 Using identity matrix for registration Qa2v: SurfXYZ to VolCRS: -- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; -- subjects dir /Applications/freesurfer/subjects/dados_Riba/ surface value path qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh hemi lh mksurfmask 0 projfrac 0 outvol path teste_sig.mgz template path fsaverage/mri/T1.mgz --- Anat2Vol Registration (TkReg) 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; - height = 256 width = 256 depth = 256 xsize = 1.00 ysize = 1.00 zsize = 1.00 cdc = -1.00 0.00 0.00 rdc = 0.00 0.00 -1.00 sdc = 0.00 1.00 0.00 xyz0 = 0.00 0.00 0.00 Gdiag_no -1 Reading surface /Applications/freesurfer/subjects/dados_Riba//fsaverage/surf/lh.white Done reading source surface INFO: reading qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh as MGH Done loading source values (nvtxs = 163842) INFO: mapping vertices to closest voxel INFO: resampling surface to volume INFO: sampled 73965 voxels in the volume INFO: writing output volume to teste_sig.mgz done And then, use tkmedit to view it: [Fernanda-Palhanos-Mac-Pro:freesurfer/subjects/dados_Riba] fernandapalhano% tkmedit fsaverage teste_sig.mgz mghRead(/Applications/freesurfer/subjects/dados_Riba//fsaverage/mri/teste_sig.mgz, -1): could not open file Error: Loading volume teste_sig.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Am I using wrong parameters in mri_surf2vol? Thanks again, Fernanda On Mon, Feb 21, 2011 at 5:30 PM, Bruce Fischl wrote: > Hi Fernanda > > if that's a surface overlay you'll need to sample it into the volume with > mri_surf2vol > > cheers > Bruce > > > > On Mon, 21 Feb 2011, Fernanda Palhano wrote: > > Hello, >> >> Does anyone knows if is it possible to overlay the surface file sig.mgh >> onto >> a T1 vol? >> I tried the command: >> tkmedit fsaverage T1.mgz -fthresh 2 -fmax 5 -overlay >> qdec/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh (where 2 and 5 were >> the thresholds I used in qdec), >> but it seems like I have only one point of the sig.mgh (in the slice 128) >> which is outside the volume. >> There's another way to do this? >> >> Thanks for the help! >> >> Fernanda >> >> > > 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] mri_surfcluster question
Hello, I'm running a cortical thickness analysis using Qdec. When I do Find Clusters and Go to Max, I obtain 9 clusters (min threshold 3, max threshold 5): Generating cluster stats using min threshold of 3... Found 9 clusters Contrast: 'lh-Diff-grupo1-grupo2-Intercept-thickness', 10fwhm, DOF: 30 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation - --- -- - - -- 18.8371 89238 5.07 -28.2 12.0 -14.5 16 insula 2 -5.3729 64233428.45 -35.4 50.5 -8.5 583 parsorbitalis 3 -5.1786 73273192.98-8.0 46.4 -13.0 292 medialorbitofrontal 4 -3.8763 121706 38.22 -19.6 61.01.5 53 rostralmiddlefrontal 5 -3.8612 93042 93.07 -23.8 40.2 -11.0 153 lateralorbitofrontal 6 -3.5732 14941 41.60-7.0 41.1 -22.2 79 medialorbitofrontal 73.3511 160348 0.34 -30.3 10.7 -14.11 insula 83.3502 111085 31.96 -33.8 -13.2 -4.6 68 insula 9 -3.2412 99299 19.05 -34.6 47.2 18.4 26 rostralmiddlefrontal Why when using the command line mri_surfcluster with the same thresholds I do not have the same results (same clusters)? # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.48 2010/04/12 17:36:58 greve Exp $ # $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ # CreationTime 2011/05/02-19:07:52-GMT # cmdline mri_surfcluster --in qdec/lh_g1_g2/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh --subject fsaverage --hemi lh --thmin 3 --thmax 5 --sign abs --annot aparc --sum summary_3_5 --olab lh_g1_g2 # cwd /Applications/freesurfer/subjects/dados # sysname Darwin # hostname Fernanda-Palhanos-Mac-Pro.local # machine i386 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input qdec/lh_g1_g2/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # annot aparc # SUBJECTS_DIR /Applications/freesurfer/subjects/dados # Minimum Threshold 3 # Maximum Threshold 5 # Threshold Signabs # AdjustThreshWhenOneTail 1 # Area Threshold0 mm^2 # Overall max 8.83713 at vertex 89238 # Overall min -5.37286 at vertex 64233 # NClusters 12 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs Annot 1 -4.995 29209398.78-33.5 48.6 -10.8 548 rostralmiddlefrontal 2 -4.995 16744185.39 -8.3 45.3 -12.5 283 medialorbitofrontal 34.914 28205 0.34-28.4 11.8 -11.8 1 insula 44.850 22061 2.37-26.89.7 -13.8 8 insula 54.512 52766 0.38-29.8 11.0 -11.4 1 insula 6 -3.876 121706 38.22-19.4 59.1 -1.653 rostralmiddlefrontal 7 -3.861 93042 93.07-23.5 38.5 -11.2 153 lateralorbitofrontal 83.691 89239 0.68-27.5 11.7 -12.5 2 insula 9 -3.573 14941 41.60 -7.0 38.8 -20.679 medialorbitofrontal 103.351 160348 0.34-29.99.7 -12.3 1 insula 113.350 111085 31.96-33.5 -12.9 -3.268 insula 12 -3.241 99299 19.05-34.2 46.6 14.726 rostralmiddlefrontal In the right hemisphere I have the same problem: Generating cluster stats using min threshold of 3... Found 6 clusters Contrast: 'rh-Diff-grupo1-grupo2-Intercept-thickness', 10fwhm, DOF: 30 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation - --- -- - - -- 1 16.5175 22102 2.8933.5 10.7 -13.07 insula 26.0843 160464 1.0830.8 13.1 -13.13 insula 3 -5.9997 62430 1.0836.13.3 -19.13 insula 4 -3.3483 60593 24.7535.9 55.5 -7.6 36 rostralmiddlefrontal 53.2156 23631 10.7819.8 -65.11.5 15 lingual 63.1968 120630 0.2829.1 11.5 -15.81 insula cmdline mri_surfcluster --in qdec/rh_g1_g2/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh --subject fsaverage --hemi rh --thmin 3 --thmax 5 --sign abs --annot aparc --sum rh_summary_3_5 --olab rh_g1_g2 # cwd /Applications/freesurfer/subjects/dados # sysname Darwin # hostname Fernanda-Palhanos-Mac-Pro.local # machine i386 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input qdec/rh_g1_g2/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /Applications/freesurfer/subjects/dados # Minimum Threshold 3 # Maximum Thre
Re: [Freesurfer] Interpreting results from Qdec
Hello, I have a follow up question about using mri_segstats. What is the difference between to use mri_segstats --in SUBJECT/surf/lh.thickness.fwhm10.fsaverage.mgh --slabel fsaverage lh ROI-drawn-on-QDEC-brain.label --avgwf lhSupTempctrls.txt and to use mri_label2label --srclabel fsaverage/label/ROI-drawn-on-QDEC-brain.label --srcsubject fsaverage --trgsubject SUBJECT --trglabel SUBJECT/label/ROI-drawn-on-QDEC-brain.label --regmethod surface --hemi lh and then mris_anatomical_stats -l SUBJECT/label/ROI-drawn-on-QDEC-brain.label -t lh.thickness -b -f SUBJECT/stats/ROI-drawn-on-QDEC-brain.label.stats SUBJECT lh. Should I have the same results using both? Thanks, Fernanda On Wed, Apr 27, 2011 at 2:12 PM, Gallen, Courtney (NIH/NIDA) [F] < galle...@nida.nih.gov> wrote: > Hi Doug > > Have a follow up question regarding significance levels in Qdec related to > extracting means from ROIs, etc. I'm posting to the entire mailing list in > case anyone else has ideas. > > Basically, I extracted mean volumes (from my set of participants) of ROIs > for which Qdec reports an interaction between two variables. I want to look > at these mean volumes in something like SPSS to see what is driving the > interaction/generate figures, etc. > > I'm having an issue with one such ROI, in that when I extract the mean > volumes and look for this interaction in SPSS, it is not significant (p ~ > 0.5, so really not significant at all). Is there any way that an ROI could > be significant in Qdec (p of 0.05, Monte Carlo sim), but not in SPSS when I > extract means for each participant? > > Let me know if this isn't clear. Any thoughts would be appreciated! > Courtney > > > Courtney Gallen > Post-baccalaureate IRTA > Neuroimaging Research Branch > National Institute on Drug Abuse (IRP) > 251 Bayview Blvd > Suite 200 > Baltimore, MD 21224 > Tel: (443) 740-2631 > > -Original Message- > From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, April 26, 2011 1:06 PM > To: Gallen, Courtney (NIH/NIDA) [F] > Subject: Re: [Freesurfer] Interpreting results from Qdec > > Those are the values outside (first column) and inside (2nd col) the > ROI. You can add "--id 1" to only report the values inside the ROI. > > doug > > On 4/26/11 1:02 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: > > It worked! > > Now, last question. The txt file has two separate values (?averages). > What do they each represent? > > > > -Original Message- > > From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] > > Sent: Tuesday, April 26, 2011 12:53 PM > > To: Gallen, Courtney (NIH/NIDA) [F] > > Subject: Re: [Freesurfer] Interpreting results from Qdec > > > > try "--slabel fsaverage lh ROI-drawn-on-QDEC-brain.label" > > > > > > On 4/26/11 12:52 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: > >> Actually, I hope I'm wrong about what I thought below. If I specify > individual subject's label and run: > >> > >> mri_segstats --in > /prot/Mprot/CTQ/freesurferDone/8579/surf/lh.volume.fwhm10.fsaverage.mgh > --slabel 8579 lh > /prot/Mprot/CTQ/freesurferDone/8579/label/lh.SupTemp_CTQxBDNFctrls.label > --avgwf lhSupTempctrls.txt > >> > >> I still get the same error about dimension mismatch > >> > >> > >> -Original Message- > >> From: Gallen, Courtney (NIH/NIDA) [F] > >> Sent: Tuesday, April 26, 2011 12:43 PM > >> To: 'Douglas Greve' > >> Subject: RE: [Freesurfer] Interpreting results from Qdec > >> > >> Ah I think I see the problem now. > >> > >> The label I originally specified is the general label created from the > ROI drawing in Qdec. Instead, I should use the individual subject's label > (from 'Map Label to Subjects') instead, right? > >> > >> Thank you! > >> > >> -Original Message- > >> From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] > >> Sent: Tuesday, April 26, 2011 12:38 PM > >> To: Gallen, Courtney (NIH/NIDA) [F] > >> Subject: Re: [Freesurfer] Interpreting results from Qdec > >> > >> You have to use the subject that matches the input, fsaverage in this > >> case. How did you define your label? If you defined it on subject 123, > >> you can transfer it to fsaverage using mri_label2label. > >> doug > >> > >> On 4/26/11 12:28 PM, Gallen, Courtney (NIH/NIDA) [F] wrote: > >>> Not a problem at all! > >>> > >>> If I use --in, I get an error saying that there is a dimension mismatch > between input volume and seg. > >>> > >>> Any other thoughts? Thanks again! > >>> > >>> -Original Message- > >>> From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] > >>> Sent: Tuesday, April 26, 2011 11:40 AM > >>> To: Gallen, Courtney (NIH/NIDA) [F] > >>> Subject: Re: [Freesurfer] Interpreting results from Qdec > >>> > >>> > >>> Hi Courtney, sorry for the delay. If more than a few days go by without > >>> a response, feel free to repost -- I promise not to get annoyed! > >>> Sometimes, things get pushed up and out of my mail browser window, and > I > >>> often don't get back to them. Sorry! > >>> > >>> To answer your question, try using -
[Freesurfer] mri_segstats error
Hello, I'm trying to use mri_segstats to obtain some subcortical volume stats. When running the command line both in the tutorial data or in my own data, I have the follow error: ERROR: could not open stats/aseg.stats for writing [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial] fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 004 sysname Darwin hostname Fernanda-Palhanos-Mac-Pro.local machine i386 user fernandapalhano atlas_icv (eTIV) = 1792580 mm^3(det: 1.086761 ) ERROR: could not open stats/aseg.stats for writing Any ideas? Thanks, Fernanda ___ 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] Question about volumetric group analysis
Hello, I have two questions about volumetric analysis: First: Are the volume measures in the files aseg.stats or ?h.aparc.stats (Gray Matter Volume) already normalized by ICV? Or should I divide all the structure volumes which I want to compare between subjects by the ICV of each subject? Second: When comparing gray matter volumes the correct is use the ICV or the total cortical gray matter volume to normalize? And if I have to use the total cortical gray matter volume, how can I obtain it? I know that this information is in the aseg.stats file, but I was wondering if I can use asegstats2table to extract it. Thank you very much, Fernanda ___ 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] Help on QDEC: Obtainign mean, sd and p-values from glm result
Hello, I've just started using freesurfer. I've reading the mail list wich helps me a lot, but I can't find how I can obtain a table with the values of my glm analysis. For exemple, in the Qdec's tutorial I have a surface that answer the question "Does the correlation between thickness and age differ from zero?" It's possible to see this data like a table: region mean sdp-value precentral xx x Or at least obtain those values individually? thank you very much in advance, Fernanda ___ 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] ERROR: _FindFacePath
Hello, When trying running recon-all I am getting the following error: #...@# Fix Topology rh Sat Aug 14 04:15:31 BRT 2010 ERROR: _FindFacePath: could not find path! Darwin Fernanda-Palhanos-Mac-Pro.local 10.4.0 Darwin Kernel Version 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 i386 recon-all exited with ERRORS at Sat Aug 14 04:26:14 BRT 2010 I've tryed twice, but i get the same error. Could anyone help me? Thanks in advance, Fernanda ___ 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] Clusters - Qdec 1.4
Hello All, Does anyone know if it's possible to automatically create labels for the clusters found with the new feature in Qdec 1.4, *Find Clusters and Goto Max*? I want to map the clusters onto all my subjects and then use * mris_anatomical_stats* to get average thickness and st. deviation for each one. Thanks in advance, Fernanda Palhano ___ 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.
