Freesurfer

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30132 discussions

bbregister
by MCLAREN, Donald 20 Nov '12

20 Nov '12

Doug, I received this question from a colleague, "Exactly which segmentation file from "recon -all" is being used in the "bbregister" command?" Thanks, Donald

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Training Comparison
by Ryan 20 Nov '12

20 Nov '12

Hello all, I'm doing a training comparison (training type A vs. type B), and I created thickness difference files (the rate files from the long_mris_slopes command) for each subject. How can I conduct an FSGD analysis with these thickness difference files? I tried replacing all of the lh.thickness and rh.thickness files with the lh.long.thickness-rate files, but it gives me the following error: MRISreadBinaryCurvature: incompatible vertex number in file /Applications/freesurfer/subjects/7107-60_base/surf/lh.thickness ERROR: reading curvature file -- -Ryan

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Re: [Freesurfer] Vertex wise analysis and area/pial area/volume interpretation
by S.E. Mous 20 Nov '12

20 Nov '12

Dear FreeSurfers, I didn't notice a resolution to this thread. I'm experiencing the same 'problem'; When I run Qdec and perform a Monte Carlo correction of 1.3, the terminal window output gives me the following clusters and values (during the MC correction I used the 'abs' option): # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.665 132680 2413.29 -41.5 2.8 24.3 0.00010 0.00000 0.00020 4785 precentral 2 -3.915 4012 1620.38 -30.7 -26.1 61.8 0.00010 0.00000 0.00020 3811 postcentral 3 -3.257 53060 1559.53 -51.7 -0.2 -23.9 0.00010 0.00000 0.00020 2447 middletemporal 4 -2.846 100336 1266.09 -17.0 30.2 44.1 0.00240 0.00180 0.00300 2203 superiorfrontal 5 -2.676 4834 855.91 -19.3 30.5 -14.5 0.03440 0.03210 0.03670 1194 lateralorbitofrontal But when (after performing MC correction) I hit the button 'Find Clusters and Goto Max' I get different (less) clusters and different Max and coordinate values: ============================================================ Generating cluster stats using min threshold of 2... Found 4 clusters Contrast: 'lh-Avg-thickness-sumD_adh_5_add1_SQRT-Cor', 10fwhm, DOF: 360 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -4.0000 0 2413.29 -36.8 -18.3 64.5 4785 precentral 2 -4.0000 17 1620.38 -21.0 -34.8 68.6 3811 postcentral 3 -4.0000 39 1559.53 -53.5 -20.2 -25.5 2447 middletemporal 4 -2.6198 21 1266.09 -6.6 33.8 49.8 2203 superiorfrontal ============================================================ Could you please explain this difference in output and why the Max and coordinate values differ? Thank you very much for your help! Best, Sabine Mous -- Sabine Mous, MSc Department of Child & Adolescent Psychiatry/Psychology PhD student, Generation R Study Erasmus MC, room AE-005 P.O.Box 2040 3000 CA Rotterdam The Netherlands Phone: (+31) 10 7038019 E-mail: s.mous(a)erasmusmc.nl http://www.erasmusmc.nl/kinderenjeugdpsychiatrie http://www.generationr.nl/

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Re: [Freesurfer] Subgroup analysis
by Mahinda Yogarajah 20 Nov '12

20 Nov '12

Hi Donald and Doug, Thanks for advice. Can I be a little bit clearer as I suspect I need a little more guidance. When comparing controls (gp c) and whole patient group (gp p) I see interesting differences in area (DOSS model after checking for no interaction and with age and ICV as correction factors). I also see an interesting interaction between age and group (DODS model with ICV as nuisance factor) such that that thickness correlates stronger with age in one group compared to another group. The patient group can be split into 4 subgroups (gp p1 to gp p4) depending on level of an endogenous substance. I want to see whether when running gp c against gp p1, if the interaction between group and age (for thickness) is stronger/weaker than the interaction when running gp p4 against gp c. I also want to see whether differences in area between a subgroup and controls are bigger/smaller compared to differences between other subgps and controls. To do this can I use the original method (granted power will b smaller) or if I follow the method suggested by Donald should I demean individually within subgroups. Also is this kind of model qdec friendly, and if not could you offer any guidance on design matrix and contrasts. Hope i make some sense ! Thanks. Mahinda

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Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 20 Nov '12

20 Nov '12

Please find the Xtmp.mat in the attachment.Thank you, Doug. Best Wei ---- Can you send me the Xtmp.mat file? dloug On 11/16/2012 01:01 PM, Zhou, Wei wrote: > Hi Doug, > > It seems the previous fieldsign-sess problem is due to that I stored > data on one server while freesurfer is on the other server. > But when I put the data and freesurfer on the same server and run the > retinotopy analysis again, it reported fail msg for "selxavg3-ses" : > -- > ntptot = 80, nX = 27, DOF = 53 > Saving X matrix to > /media/local_home/zhouw4/testf/retinotopy/SUBJ01/bold/rtopy.self.lh/Xtmp.mat > Error using svd > Input to SVD must not contain NaN or Inf. > > Error in cond (line 39) > s = svd(A); > > Error in fast_selxavg3 (line 254) > XCond = cond(XtX); > --- > I checked Xtmp.mat. There is NaN in Xn and XtX. > My rtopy par is: eccen and pos. > > Would you please give me some idea about this error? > > Best > Wei > > >> > Try using this version > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fieldsign-sess > > doug > > On 11/01/2012 11:47 AM, Zhou, Wei wrote: > > Hi Doug, > > > > The subject name for structural is "SUBJ1" when I did recon-all, which > > is also the content of file "subjectname". My dir structures of > > "structural" and "retinotopy" are the same as > > http://www.alivelearn.net/?p=65 . "SUBJ1" is stored under > > "structural". if I set SUBJECTS_DIR as "....../structural", > > $SUBJECT_DIR/SUBJ1 does exist, then still I get the same error msg. > > > > The following is the log file: > > > > fieldsign-sess log file $Id: fieldsign-sess,v 1.2 2010/05/04 22:00:18 > > greve Exp $ Thu Nov 1 10:36:52 CDT 2012 Linux rii-appserv-02 > > 2.6.32-279.11.1.el6.x86_64 #1 SMP Sat Sep 22 07:10:26 EDT 2012 x86_64 > > x86_64 x86_64 GNU/Linux /media/users/zhouw4/testf/retinotopy > > /usr/local/freesurfer/fsfast/bin/fieldsign-sess -a rtopy.self.lh > > -occip -s SUBJ1 uid=20120(zhouw4) gid=22000(rii_users) > > groups=22000(rii_users),21100(rii_appservers),23000(domain^users) > > context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 > > > > Best > > Wei > > > > > > >What is the name of FreeSurfer subject? This is not necessarily the > > same>> > > >as SUBJ01 in your command line below. That is the session (which may or > > >may not be the same as the "subject name"). What ever the subjectname > > is, does SUBJECT_DIR/subject exist? > > On 10/31/2012 03:07 PM, Zhou, Wei wrote: > > > > > > Hi, Doug > > > > > > Thank you for your reply. I have tried exporting SUBJECTS_DIR to the > > > directory of upper fold, retinotopy or SUBJ01 But none of them works. > > > Still the same error msg. > > > > > > So what should SUBJECTS_DIR be exported to for this analysis? > > > > > > Best > > > > > > Wei > > > > > > > > > > > > >Hi Wei, this is a bug in the error msg. It is trying to say that your > > > >source subject is not in the $SUBJECTS_DIR. > > > >doug > > > > > > >On 10/27/2012 02:27 PM, Zhou, Wei wrote: > > > > Dear freesurfers, > > > > > > > > I am trying retinotopy analysis in freesurfer. For > > "fieldsign-sess", I > > > > encounter the following problem when I type "fieldsign-sess -a > > > > rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a > > rtopy.self.lh > > > > -occip -sf sessid": > > > > > > > > > > */media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* > > > > *subject: Undefined variable.* > > > > > > > > my structure of retinotopy fold is : > > > > retinotopy > > > > | |--sessid > > > > |--SUBJ01 > > > > |--subjectname > > > > > > > > |--bold > > > > |--001 > > > > |--f.nii > > > > |--rtopy.par| > > > > > > > > I really appreciate it if you could give me some idea about that > > > > problem. Thanks a lot in advance. > > > > > > > > Best > > > > Wei Zhou > > > > Medical Physics Ph.D. Student > > > > Diagnostic Imaging Track > > > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > gr...(a)nmr.mgh.harvard.edu > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > Best > > Wei Zhou > > Medical Physics Ph.D. Student > > cgxz...(a)gmail.com<mailto:cgxz...@gmail.com> > > zho...(a)livemail.uthscsa.edu<mailto:zho...@livemail.uthscsa.edu> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > Best > Wei Zhou > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Best Wei Zhou

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Converting SPM2 File to FreeSurfer Space
by Eun Young Choi 20 Nov '12

20 Nov '12

Hi all, I'd like to convert SPM2 spmT files to FreeSurfer space. I have a Colin template brain available to help with the conversion, as well. Has anyone done this before? Any suggestions on how to do this? Many thanks in advance, Eun Young

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flip brain
by Chen, Xiaoyan 20 Nov '12

20 Nov '12

Dear Freesurfer experts, I have a general question regarding data analysis. Our group has collected data from patients with OA, some of them received treatment on their left leg, some of them on their right leg. We would like to flip the brain for the people that received treatment on their left leg to match the right leg group. Next, we would like perform group analysis on them. My question is, when should we flip the brain for the left leg group patients? Should we flip the raw images before we do any preprocessing at the individual level? Or should we flip the first level contrast images when we get some results for each of these subjects? I tried to flip the contrast images, but it seems to give me a lot of error at the second level group analysis level. It says that the flipped contrast image does not match the unflipped contrast image in orientation. Thank you very much. Helen

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Red Hat Enterprise Linux 6?
by Brain Apprentice 20 Nov '12

20 Nov '12

Hi Surfers, I was wondering if FreeSurfer v5.1.0 (CentOS 4 x86 (64b)) or V5.X will work on Red Hat Enterprise Linux 6? The reason I ask is that the supercomputer at Brigham Young University is going through a major overhaul: changing the OS, adding more nodes, and adding more storage. I am just curious what type of problems I will run into. I know I will need to rerun all brains through the new system but more concerning to me is if I can run FreeSurfer at all on the new system. Thanks in advance for any suggestions or insights you can offer.

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trac-all -bedp post processing e-mail notification
by Loi 20 Nov '12

20 Nov '12

Hello FreeSurfer experts, I am wondering if it is possible to run trac-all -bedp without generating the email notification at the end of the post-processing stage? After submitting a long list of -bedp jobs to the local cluster, I received a message from our IT center reporting being spammed by the Mail Delivery System with the following message: - - This message was created automatically by mail delivery software. A message that you sent could not be delivered to one or more of its recipients. This is a permanent error. The following address(es) failed: 'myusername'@fmrib.ox.ac.uk - - I am assuming it is the -bedp e-mail notification that is bouncing. Thanks for the help Joy-Loi

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tksurfer crashes
by Righart, Ruthger Dr. 20 Nov '12

20 Nov '12

Dear Freesurfer experts, I have a problem with Tksurfer. Whereas this worked previously fine it suddenly crashes every time I try to start it. This happens with every subject or fsaverage. A similar problem was reported before with similar terminal output but unfortunately I could not find a solution to this problem in the mailing list. Any suggestions are welcome! Ruthger Righart Hi Michelle, hmmm, no idea. Do you want to upload the the subject and we'll see if we can replicate the problem? Do you have enough memory on that machine? Bruce On Mon, 19 Mar 2012, Michelle Umali wrote: Hi Freesurfers, I've been using Freesurfer for a while, and have had no trouble with launching tksurfer. But recently I have tried to view an inflated hemisphere of a subject I have had no problem viewing before. The window no longer opens. This the case for all of my subjects, with whom I have had no previous problems. Any suggestions would be most welcome. Thanks very much. Michelle Below is the terminal output. After this it just returns to the prompt without any error message.. /usr/local/freesurfer/subjects> tksurfer ld07 lh inflated subject is ld07 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=160638, faces=321272 surfer: double buffered window surfer: tkoInitWindow(ld07)

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