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Difference between lh.thickness file and lh.thickness.fsaverage.mgh file
by Zhiliang Long 23 Apr '17

23 Apr '17

Dear FS experts: I conducted recon-all analysis on my own subjects, and found that there are several kinds of thickness files, such as the lh.thickness file and lh.thickness.fsaverage file. By using MATLAB scripts implemented in FS, different numbers of vertex were found between the two files. What I am thinking is that the lh.thickness file is the individual thickness map (It has not been transformed into fsaverage space), while the lh.thickness.fsaverage.mgh is the thickness map in fsaverage space. Is that correct? Best, Zhiliang

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R: R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt
by stdp82＠virgilio.it 23 Apr '17

23 Apr '17

Dear list and Eugenio, I have run for each subject mri_label2vol --label SUBJ/label/rh.perirhinal_exvivo.thresh.label --regheader SUBJ/mri/norm.mgz --fill-ribbon --subject SUBJ --hemi rh --o SUBJ/mri/rh.perirhinal.nii.gz next, to use FS-FAST on perihrinal.nii.gz, I have run fcseed-config -seg SUBJ/mri/lh.perirhinal.nii.gz -fcname L_Perirhinal.dat -fsd rest -mean -cfg mean.L_Perirhinal.config This error occurs: ERROR: no segmentations IDs (-segid) or ROI (-roi) specified What's should I do? Thanks Stefano On Mon, 06 Feb 2017 13:59:38 -0800 Do you mean to use them as seeds in FSFAST? You'll need to map them into the conformed space using mri_label2vol with the --regheader option (see the --help); view the volume to make sure it looks ok. Then run fcseed-config specifying the volume with -seg and the code with segid ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 6-feb-2017 22.27 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt Thank you very much.Could you provide me any suggestion to extract CA1 left or CA1 right?And how can I use them in FAST? By codes?Regards,Stefano ----Messaggio originale---- Da: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Data: 6-feb-2017 17.42 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Hipposubfields in FreeSuerferColorLUT.txt You would extract CA1 left from lh.hippoSfLabels-T1.v10.mgz and CA1 right from rh.hippoSfLabels-T1.v10.mgz (assuming you’ve used T1s to segment the subfields). Cheers, /E Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Feb 2017, at 16:17, stdp82(a)virgilio.it wrote: Thanks Eugenio for your response. My apologies but this matter is unclear to me. If I would use results for FS-FAST how I can identify for example CA1 right from CA1 left? Additionally, for enthorinal which is the correct code in FAST? Stefano ----Messaggio originale---- Da: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Data: 6-feb-2017 15.54 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Hipposubfields in FreeSuerferColorLUT.txt Ciao Stefano, The results for the left and right hippocampi are in different files, so there’s no ambiguity despite the fact that they indeed share the same label codes. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Feb 2017, at 13:18, stdp82(a)virgilio.it wrote: Hi list, within FreeSuerferColorLUT.txt, do the numbers between 200-226 descrived the hippo-subfield outputs? Additionally, how can I obtain separate right and left masks? Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)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(a)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.

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mris_label2annot not creating annot file
by Das S. 23 Apr '17

23 Apr '17

Hi, I was using the mris_label2annot to create .annot file before but now couldn't figure out why the .annot file is not being created. The mris_label2annot is giving the below output but not creating the label files. My label file names are as node-lh-xx.label and the content of ctab file as below: 0 node-lh-0 25 5 25 0 1 node-lh-1 70 0 180 0 2 node-lh-2 245 245 245 0 3 node-lh-3 205 62 78 0 4 node-lh-4 120 18 134 0 5 node-lh-5 196 58 250 0 6 node-lh-6 0 148 0 0 7 node-lh-7 220 248 164 0 8 node-lh-8 230 148 34 0 9 node-lh-9 0 118 14 0 10 node-lh-10 70 118 14 0 11 node-lh-11 122 186 220 0 12 node-lh-12 236 13 176 0 13 node-lh-13 12 48 255 0 14 node-lh-14 204 182 142 0 *********************************************************** mris_label2annot --s 100307 --h lh --no-unknown --ctab label/eq_parcellation_label/MyColorLUTleft01.txt --a eq40left --ldir label/eq_parcellation_label/left/ Reading ctab label/eq_parcellation_label/MyColorLUTleft01.txt Number of ctab entries 41 INFO: no labels specified, generating from ctab $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/koushik/Parcellation/100307 cmdline mris_label2annot --s 100307 --h lh --no-unknown --ctab label/eq_parcellation_label/MyColorLUTleft01.txt --a eq40left --ldir label/eq_parcellation_label/left/ sysname Linux hostname koushik-DQ77MK machine x86_64 user koushik subject 100307 hemi lh SUBJECTS_DIR /home/koushik/Parcellation ColorTable label/eq_parcellation_label/MyColorLUTleft01.txt AnnotName eq40left nlables 0 LabelThresh 0 0.000000 Loading /home/koushik/Parcellation/100307/surf/lh.orig Writing annot to /home/koushik/Parcellation/100307/label/lh.eq40left.annot Thanks Sarbani

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aparc files missing a comma
by Mike Schmidt 22 Apr '17

22 Apr '17

Hello FreeSurfer Developers, I'm attempting to parse stats files with regular expressions. Everything seems to work in all of the aseg and wmparc files, but the {lh,rh}.aparc{,a2009s,DKTatlas,pial}.stats files are missing a comma after "CortexVol" on line 25. This causes my regex to miss that measurement on each pass. All other lines match my regex perfectly, only CortexVol misses the comma. This is a new field in version 6; it does not exist in versions 5.2.0 and 5.3.0. This is consistent across all subjects I've viewed, and there are no errors to dig into, but I've attached the recon-all.log file and a few stats files from one of them in case they're of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_ 64-stable-pub-v6.0.0-2beb96c 2) Platform: external linux cluster, unsure exactly 3) uname -a: Linux sequoia 3.12.67-60.64.24-default #1 SMP Fri Dec 9 14:35:11 UTC 2016 (8154761) x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached, along with a few aparc files. I have added the comma using sed to all of the aparc files in our system, but I hope this is helpful in removing bugs for future use. Best wishes, Mike Schmidt

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Superior Posterior Insula and DLPFC measurements
by Guilherme Alves 22 Apr '17

22 Apr '17

Hello everyone, I’ve been having a hard time trying to figure out how to get appropriate measures of gray matter volume for both the superior posterior insula and the DLPFC. The atlases included in freesurfer don’t provide such information after the recon-all process is run. Is there a way to get accurate measures without having to manually label these areas for each subject? I’ve seen some answers on the archive defining the posterior insula as G_Ins_lg_and_S_cent_ins, but how can I isolate the superior posterior insula? Is there a way to create a new label based on a combination of pre-existing labels? Thanks in advance, Guilherme.

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Need help to run freesurfer
by Ramesh Babu 22 Apr '17

22 Apr '17

Dear Experts, I have installed in /usr/local/freesurfer. I am trying to follow the command given in the freesurfer web page. $> export FREESURFER_HOME=/usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh But I could not figure out the .sh file in the freesurfer folder. Please see the list of files in the freesurfer folder given below. List of files in the freesurfer folder; /usr/local/freesurfer/average /usr/local/freesurfer/fsafd /usr/local/freesurfer/fsfast /usr/local/freesurfer/lib /usr/local/freesurfer/sessions /usr/local/freesurfer/tktools /usr/local/freesurfer/trctrain /usr/local/freesurfer/DefectLUT.txt /usr/local/freesurfer/FreeSurferColorLUT.txt /usr/local/freesurfer/FreeSurferEnv.csh /usr/local/freesurfer/LICENSE /usr/local/freesurfer/SetUpFreeSurfer.csh /usr/local/freesurfer/sources.csh /usr/local/freesurfer/sources.sh /usr/local/freesurfer/tkmeditParcColorsCMA /usr/local/freesurfer/VERSION /usr/local/freesurfer/WMParcStatsLUT.txt You can notice that there is no SetUpFreeSurfer.sh file. Details about my pc; Ubuntu 16.04 LTS, 64 bit is installed. Running w8.1 via virtual box. Freesurfer is installed in Ubuntu OS. I am using bash shell. pc@RB:~$ echo $0 bash pc@RB:~$ echo $SHELL /bin/bash pc@RB:~$ ps -p "$$" PID TTY TIME CMD 3706 pts/1 00:00:00 bash Need your help to run freesurfer in my pc. Thanks in advance Ramesh

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Multiple comparisons
by Laura Ferrero Montes 22 Apr '17

22 Apr '17

Dear FS team, I would like to correct for multiple comparisons after I run command-line GLM analysis on stats tables. I would like to make a second level analysis between a control group and an autism group. I would like to know if there is a command-line in FreeSurfer or if there is any program or toolkit in Matlab that allows to do that. Thank you, Laura

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mri_glmfit error with aparc table flag
by miracle ozzoude 21 Apr '17

21 Apr '17

Hello freesurfer, I am trying to run mri_glmfit with the --table flag. My aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness values for 32 subjects. I ran the glm command and received an error. Please, how can i solve this issue? I have included my command, fsgd file, contrast matrix and error below. Thanks Best, Paul GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir ERROR= "gdfRead(): reading age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 39.9375 17.3312 Class Means of each Continuous Variable 1 Group1 35.6316 2 Group2 46.2308 INFO: gd2mtx_method is dods Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Users/MiracleOz/Documents/improvervsdeclinermri cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.glmdir sysname Darwin hostname MacBook-Pro.local machine x86_64 user MiracleOz FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt logyflag 0 usedti 0 FSGD age.fsgd labelmask /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.thickness.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.thickness.glmdir Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt Found 66 data colums Found 0 data rows INFO: gd2mtx_method is dods Saving design matrix to lh.thickness.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 32.2165 Matrix condition is 20734.7 Found 149955 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 66 search space = 82219.962936 ERROR: dimension mismatch between y and X. y has 0 inputs, X has 32 rows." FSGD file: GroupDescriptorFile 1 Title MOT Class Group1 Class Group2 Variables Age Input 01053p Group1 23 Input 01054p Group1 43 Input 01061p Group2 39 Input 01062p Group2 19 Input 01074p Group2 28 .............. (I have more participants) CONTRAST MATRIX: 1 -1 0 0

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help mri_surf2vol
by pierre deman-kibleur 21 Apr '17

21 Apr '17

Hi, Is there a way to have the destrieux parcellation on a volume format ? .nii for example. I tried to used mri_surf2vol without success for now: mri_surf2vol --subject 0001GRE_25-11-2014 --merge /home/b67-belledone/freesurfer/subjects/0001GRE_25-11-2014/mri/T1.mgz --so /home/b67-belledone/freesurfer/subjects/0001GRE_25-11-2014/surf/lh.orig /home/b67-belledone/freesurfer/subjects/0001GRE_25-11-2014/label/lh.aparc.a2009s.annot --o /tmp/test.nii Regards, Pierre -- DEMAN Pierre Mobile : +33 7 82 57 80 94

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Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast
by Antonin Skoch 20 Apr '17

20 Apr '17

Dear Bruce, I am uploading 3 example subjects processed both by v5.3 and v6.0 I referred to in the screenshots in my previous posts: Subj 1 - large leak of white surface outside brain in v6.0, not present in v5.3. RAS coords -53,-1,75 Subj 2 - another measurement of identical subject - white surface is leaking at three spots dramatically outwards towards pial surface in v6.0. RAS coords -48,-2,64 Subj 3 - leak of white surface outside brain. Both v5.3 and v6.0 has error in white surface, but the error is much larger in v6.0. RAS coords 48,5,78 The v6.0 version is without removing -mprage. Removing -mprage in v6.0 caused only very small change in brain.mgz, the filtering is still much higher than in v5.3 and still causes the white matter surface leak. The subjects are in files mri_normalize_v5.3.tar.gz and mri_normalize_v6.0.tar.gz. I would very welcome any suggestions how to: 1. Prevent new white surface errors in v6.0 in subjects previously processed and edited by v5.3 2. How to make edits to modify white/pial surface location where wm.mgz editing is not sufficient. I tried workaround of directly editing 001.mgz as I discussed in thread http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html This is very time consuming. Better way is maybe to consider implementation of option for mris_make_surfaces similar to -overlay option for cases where wm.mgz voxels have value 1 as I discussed here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52730.html Antonin Hi Antonin yes, the -mprage flag is likely to be at least one source of the differences. It makes the normalization more aggressive (since mprage trades higher CNR for lower SNR). I'm surprised removing it didn't help. I think that changing things like wlo could also help depending on how wrong the normalization is. Upload a subject and I'll take a look cheers Bruce On Thu, 20 Apr 2017, Antonin Skoch wrote: Dear David, thank you for the feedback; I saw your posts concerning edits and responded to them, see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html Just my case is not concerning poor response to the edits (which I believe is not systematically different between 5.3 and 6.0), my concern is that the data processed by v6.0 need much more wm.mgz edits than data processed by v5.3. I think that my issue lies in -normalization2 step of recon-all. One of the difference between v5.3 and v6.0 is that by default the -mprage flag is passed to mri_normalize. This affects several parameters inside mri_normalize. I tried to reprocess my subjects using v6.0 with -no-mprage, but unfortunately this did not help. See the example screenshots processed by v5.3 and v6.0 with -no-mprage: The brain.mgz is still more aggressively filtered in v6.0 and there is much more prominent leak of ?h.white outside brain, which is probably caused by extended filtration which affects GM/WM contrast. Looking at the source code of mri_normalize.c I did not comprehend where the basis of the issue lies, but in any case there are big differences in mri_normalize.c code between versions. Antonin From: David Semanek <seman...(a)nyspi.columbia.edu> To: Antonin Skoch <a...(a)ikem.cz>, "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: 4/20/2017 3:41 PM Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast Agreed. A validated protocol run on a very large group of subjects in 5.3 was attempted with similar data in 6.0 and not only was the longitudinal edit stream nearly non-functional for white matter edits, cross edit performance was disappointing. I am currently waiting on a response to these potential issues before pursuing further work with 6.0. Best, David P. Semanek, HCISPP Research Technician, Posner Lab Division of Child and Adolescent Psychiatry Columbia University Medical Center New York State Psychiatric Institute 1051 Riverside Drive, Pardes Bldg. Rm. 2424 New York, NY 10032 PH: (646) 774-5885 IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From: Antonin Skoch <a...(a)ikem.cz> Date: Wednesday, April 19, 2017 at 5:23 PM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast Dear experts, I am sending just one more example to illustrate issue with white surface estimation in v6.0. See the attached screenshots: In v6.0 there seems to be insufficient contrast in brain.finalsurfs.mgz, so the white surface is leaking at three spots dramatically outwards towards pial surface. The white surface in v5.3 looks much more anatomically relevant in the same spot. Could you please comment on how to avoid such issues in v.6.0? Regards, Antonin Skoch

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