Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

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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Re: [Freesurfer] error loading datatable in qdec
by Shantanu Ghosh 19 Nov '12

19 Nov '12

As far as I can see the levels file should have Male Female <newline> as its contents. Check if the <category> you have used in the qdec.table.dat file, is it the with same name? E.g. if you have the field as SEX, then the <category.levels> file should be called <SEX.levels> Hth, Shantanu PS: could you CC freesurfer list as well? On Mon, November 19, 2012 5:06 pm, pietro de rossi wrote: > HI....I solved the problem with the dat file...but I now have a problem > with the .levels files... > > I get this > > Loading data table > /Users/derossip/desktop/Subjects_ABC_Proc/qdec/ABC_Cortex.qdec.dat... > Number of columns: 7 > fsid column: 1 > Number of factors: 6 > Number of subjects: 20 > Reading discrete factor levels from config file > /Users/derossip/desktop/Subjects_ABC_Proc/qdec/SEX.levels > Female > done. > ERROR: /Users/derossip/desktop/Subjects_ABC_Proc/qdec/SEX.levels is > invalid. Must have at least two levels. > Error loading the data table. > > although there are two levels in the .levels file....how is that possible? > > 2012/11/19 pietro de rossi <derossi05(a)gmail.com> > >> thanks...I'll try... and let you know... >> >> >> 2012/11/19 Shantanu Ghosh <shantanu(a)nmr.mgh.harvard.edu> >> >>> Is >>> >>> "886 7.386721424 Male ADHD 72 8 25" your last subject? >>> >>> The emptyline must be at the end, each field by typing a space and each >>> newline should be created by typing "Enter" when you make your >>> qdec.table.dat file. >>> >>> Otherwise try copying the default qdec file from freesurfer and >>> modifying >>> it according to your data. >>> >>> Hth, >>> S. >>> >>> >>> >>> On Mon, November 19, 2012 4:12 pm, pietro de rossi wrote: >>> > I just tried but it's very weird... I get >>> > >>> > Loading data table >>> > >>> /Users/derossip/desktop/Subjects_ABC_Proc/qdec/ABC_Cortex.qdec.table.dat... >>> > Number of columns: 147 >>> > fsid column: 1 >>> > Number of factors: 146 >>> > Number of subjects: 0 >>> > ERROR: QdecDataTable::Load: number of subjects = 0 >>> > Error loading the data table. >>> > >>> > 2012/11/19 Shantanu Ghosh <shantanu(a)nmr.mgh.harvard.edu> >>> > >>> >> Hi Pietro, >>> >> >>> >> See if using an empty newline after >>> >> >>> >> 886 7.386721424 Male ADHD 72 8 25 >>> >> >>> >> in your Qdec table solves the problem. >>> >> >>> >> Hth, >>> >> Shantanu >>> >> >>> >> >>> >> On Mon, November 19, 2012 3:28 pm, pietro de rossi wrote: >>> >> > Hi all, >>> >> > >>> >> > I tried to load a tiny data table in qdec following directions on >>> the >>> >> wiki >>> >> > online >>> >> > >>> >> > I get this error >>> >> > >>> >> > Loading data table >>> >> > >>> >> >>> /Users/derossip/desktop/Subjects_ABC_Proc/qdec/ABC_Cortex.qdec.table.dat... >>> >> > QdecDataTable::Load: will attempt to open as Mac text file... >>> >> > Number of columns: 7 >>> >> > fsid column: 1 >>> >> > Number of factors: 6 >>> >> > Number of subjects: 19 >>> >> > ERROR: QdecDataTable::Load: problem parsing file >>> >> > >>> /Users/derossip/desktop/Subjects_ABC_Proc/qdec/ABC_Cortex.qdec.table.dat >>> >> > This line did not appear to end with a newline: >>> >> > 886 7.386721424 Male ADHD 72 8 25 >>> >> > Error loading the data table. >>> >> > >>> >> > also...there are 20 subjects in my data table and not just 19... >>> >> > >>> >> > is there a way I can solve this? >>> >> > >>> >> > thanks, >>> >> > >>> >> > Pietro >>> >> > >>> >> > -- >>> >> > Pietro De Rossi, MD >>> >> > ------------------------------------- >>> >> > Sapienza Università di Roma, Facoltà di Medicina e Psicologia, >>> >> > Dipartimento >>> >> > NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale >>> >> > Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma >>> >> > >>> >> > NESMOS Department (Neurosciences, Mental Health and Sensory >>> >> Functions), >>> >> > School of Medicine and Psychology, Sapienza University, >>> SantAndrea >>> >> > Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy >>> >> > >>> >> > Neurobehavioral Clinical Research Section, Social and Behavioral >>> >> Research >>> >> > Branch, National Human Genome Research Institute (NHGRI), National >>> >> > Institutes of Health (NIH), Bethesda, Maryland 20892, USA >>> >> > _______________________________________________ >>> >> > Freesurfer mailing list >>> >> > Freesurfer(a)nmr.mgh.harvard.edu >>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >>> >> >>> >> -- >>> >> Shantanu Ghosh, Ph.D. >>> >> Harvard Medical School & Massachusetts General Hospital >>> >> Martinos Center for Biomedical Imaging >>> >> >>> >> >>> >> >>> >> 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. >>> >> >>> >> >>> > >>> > >>> > -- >>> > Pietro De Rossi, MD >>> > ------------------------------------- >>> > Sapienza Università di Roma, Facoltà di Medicina e Psicologia, >>> > Dipartimento >>> > NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale >>> > Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma >>> > >>> > NESMOS Department (Neurosciences, Mental Health and Sensory >>> Functions), >>> > School of Medicine and Psychology, Sapienza University, SantAndrea >>> > Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy >>> > >>> > Neurobehavioral Clinical Research Section, Social and Behavioral >>> Research >>> > Branch, National Human Genome Research Institute (NHGRI), National >>> > Institutes of Health (NIH), Bethesda, Maryland 20892, USA >>> > >>> >>> >>> -- >>> Shantanu Ghosh, Ph.D. >>> Harvard Medical School & Massachusetts General Hospital >>> Martinos Center for Biomedical Imaging >>> >>> >> >> >> -- >> Pietro De Rossi, MD >> ------------------------------------- >> Sapienza Università di Roma, Facoltà di Medicina e Psicologia, >> Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), >> Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma >> >> NESMOS Department (Neurosciences, Mental Health and Sensory Functions), >> School of Medicine and Psychology, Sapienza University, SantAndrea >> Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy >> >> Neurobehavioral Clinical Research Section, Social and Behavioral >> Research >> Branch, National Human Genome Research Institute (NHGRI), National >> Institutes of Health (NIH), Bethesda, Maryland 20892, USA >> > > > > -- > Pietro De Rossi, MD > ------------------------------------- > Sapienza Università di Roma, Facoltà di Medicina e Psicologia, > Dipartimento > NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale > Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma > > NESMOS Department (Neurosciences, Mental Health and Sensory Functions), > School of Medicine and Psychology, Sapienza University, SantAndrea > Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy > > Neurobehavioral Clinical Research Section, Social and Behavioral Research > Branch, National Human Genome Research Institute (NHGRI), National > Institutes of Health (NIH), Bethesda, Maryland 20892, USA > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging

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error loading datatable in qdec
by pietro de rossi 19 Nov '12

19 Nov '12

Hi all, I tried to load a tiny data table in qdec following directions on the wiki online I get this error Loading data table /Users/derossip/desktop/Subjects_ABC_Proc/qdec/ABC_Cortex.qdec.table.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 7 fsid column: 1 Number of factors: 6 Number of subjects: 19 ERROR: QdecDataTable::Load: problem parsing file /Users/derossip/desktop/Subjects_ABC_Proc/qdec/ABC_Cortex.qdec.table.dat This line did not appear to end with a newline: 886 7.386721424 Male ADHD 72 8 25 Error loading the data table. also...there are 20 subjects in my data table and not just 19... is there a way I can solve this? thanks, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Problem importing DICOM
by Memarian, Negar 19 Nov '12

19 Nov '12

Hello, I'm using Freesurfer on Windows 7 using VirtualBox. I want to import DICOM files based on the "FreeSurfer Troubleshooting Reconstruction Work Flow", but I'm facing problems. This is what I have done: 1. Tried to use the source command like this: source C:\FreeSurfer_data\SetUpFreeSurfer.csh But I got this error: C:FreeSurfer_dataSetUpFreeSurfer.csh" No such file or directory 2. Tried to change directory to my subjects directory like t this: cd C:\FreeSurfer_data But got this error: C:FreeSurfer_data" No such file or directory 3. Tried importing one subject like this: recon-all -i C:\FreeSurfer_data\DICOM2 -subjid subj2 However I get this error: ERROR: cannot find C:FreeSurfer_dataDICOM2 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i 686 GNU/Linux recon-all -s exited with ERRORS at Mon Nov 19 14:50:58 EST 2012 I tried the above commands with / (slash) instead of back slash but still got similar errors. I'd appreciate your help. Thanks, Negar Negar Memarian, MASc, PhD NSERC Postdoctoral Fellow Department of Neurology David Geffen School of Medicine at UCLA Tel: (310) 206-4178 Email: nmemarian(a)mednet.ucla.edu ________________________________ IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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exporting aseg.stats values
by pietro de rossi 19 Nov '12

19 Nov '12

Hi FreeSurfer users and developers, I'm trying to export aseg.stats values for a preliminary analysis. I would like to export them to an excel spreadsheet. My command line was asegstats2table --subjects 119 123 125 135 141 145 146 147 151 159 160 163 164 167 171 174 178 186 196 198 218 221 224 225 226 227 228 229 244 249 250 269 271 280 282 296 303 305 308 311 320 324 327 328 334 335 338 339 340 343 344 345 349 352 355 360 361 373 379 382 384 386 387 388 393 394 398 399 415 430 443 450 459 461 464 465 482 501 509 515 522 525 544 577 586 597 599 636 646 681 745 792 800 830 886 --tablefile aseg.vol.sample.table --skip I get this Parsing the .stats files Skipping /users/derossip/desktop/Subjects_ABC_Proc/386/stats/aseg.stats Skipping /users/derossip/desktop/Subjects_ABC_Proc/464/stats/aseg.stats Skipping /users/derossip/desktop/Subjects_ABC_Proc/482/stats/aseg.stats Skipping /users/derossip/desktop/Subjects_ABC_Proc/501/stats/aseg.stats Building the table.. Writing the table to aseg.vol.sample.table Now....where can I physically visualize the data? Thank you verymuch, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Freesurfer November 2012