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30099 discussions

mritotal failed - help with manual registration
by will brown 24 Jan '16

24 Jan '16

Hi all, After attempting recon-all I received the error "mritotal failed, see transforms/talairach.log" etc which I understand may have something to do with bad output from registration. I've checked orig.mgz which does look out of line - the orientation is off so that it appears the subject has their head tilted off to one side (see Image1.jpg). I have tried to fix this manually with the help of this tutorial: http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview Hovever, the "movable" blurry image that I'm trying to line up with my subjects image does not match the coronal, sagittal or horizontal views, e.g. when I click "coronal" my subject is displayed correctly but the movable image is displayed horizontally (see Image2.jpg and Image3.jpg). Am I missing something obvious? (and am I even on the right track given this error?) Thanks in advance for any help. Cheers, Will

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freeview on ubuntu
by Neda Mohammadi 24 Jan '16

24 Jan '16

Dear experts, I installed FreeSurfer on Ubuntu with these commands: sudo apt-get install tcsh cd /usr/local/ sudo tar -xzvf ~/freesurfer-*.tar.gz echo "FREESURFER_HOME=/usr/local/freesurfer" >> ~/.bashrc echo 'source $FREESURFER_HOME/SetUpFreeSurfer.sh' >> ~/.bashrc sudo gedit /usr/local/freesurfer/.license sudo ln -s /usr/lib/libtiff.so.{4,3} Every thing is Ok except freeview. When I load freeview this error is appeared. freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Any guidance on this would most appreciated. Thanks in advance, -- *Best Regards,* *Neda*

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Processing .mnc files {Disarmed}
by Arindam Chatterjee 23 Jan '16

23 Jan '16

Hello Freesurfer experts, I am still learning various aspects of Freesurfer, so pardon my questions. I am trying to run recon-all on a mnc file. It is in a folder such as /Sample1/subjects/t1/t1xxxx.mnc. I am pointing my SUBJECTS_DIR to /Sample1/subjects. But when I run recon-all -s t1, I get and error - ERROR: nothing to do. Should I be storing the .mnc file in a different location? So it looks like it is not finding the .mnc file or can Freesurfer not process a .mnc file and I have to convert it to another format like .dcm? Also, if I am able to run recon-all, what output should I analyze to determine the gyrification index? Thanks in advance for any pointers. Ankita -- Arindam Chatterjee (515) 419-7384 www.linkedin.com/in/chatterjeea

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Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit
by BAUTISTA-PERPINYA Maximilià 23 Jan '16

23 Jan '16

Thank you for the reply Douglas, Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi editor, one line for each level. Same as factor 2. Max On dijous 14 gener 2016 22:20 CET, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > how many levels does factor 1 have? How did you make the factor file?> > On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote: > > Hi there experts, > > > > I'm runing qdec to analyze my subject data. I am able to import the qdec.table.dat, but the problem comes in the Design step. I select 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 'LeftAmygdala' as the continuous variable. I don't select any nuisance factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but gives me the following error: > > > > --------------------------------------------------------------------------------------------------------------- > > > > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels > > ninputs = 137 > > Checking inputs > > nframestot = 137 > > Allocing output > > Done allocing > > nframes = 137 > > Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh > > gdfReadHeader: reading /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 LeftAmygdala 1502.65 189.974 > > Class Means of each Continuous Variable > > 1 diagnosisBPD 1497.7548 > > 2 diagnosisCCP 1540.8923 > > 3 diagnosisNPC 1488.5490 > > INFO: gd2mtx_method is dods > > Reading source surface /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white > > ERROR: no contrasts specified. > > Error in Analyze: command failed: mri_glmfit --y /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf fsaverage lh > > > > --------------------------------------------------------------------------------------------------------------- > > > > Any recommendations? Any help is much appreciated :) > > > > > > Best, > > > > Max > > > > _______________________________________________> > 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 > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________> 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. -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpinya(a)etu.unistra.fr maxbauper(a)gmail.com -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpinya(a)etu.unistra.fr maxbauper(a)gmail.com

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recon-all finishing without error but happens too quickly and output not present
by AMY LIN 22 Jan '16

22 Jan '16

Hi all, I'm trying to re-run subjects through recon-all for version 5.3.0 on a Mac 10.10.5 using Centos 6 but am not getting the normal output. There seems to be several strange things happening. The process ends almost instantaneously and says that it finished without error, so I don't get any errors or warnings. The correct subject directory folders are created (mri, bem, scripts, etc), but most of them are empty. The only folder that has anything in them are the scripts folder and the mri folder, which has the orig and transforms folders and are pretty much empty. It seems that the program is only running the mri_convert command on the 001.mgz file, writing the output to the folder that I've specified and then finishes without error. I've tried to run the commands on both local and remote servers to rule out an issue with the server and from different user accounts to rule out permission issues as I am a new lab member. I've also tried several different subjects to rule out problems with the scans. Also, these subjects have been run previously on an older version of FS, so the problem is likely not with the scans themselves. Any help at all would be much appreciated!

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HippocampalSubfields only generates lh
by Jiook Cha 22 Jan '16

22 Jan '16

Hi Iglesias, I recently tried HippocampalSubfields in freesurfer 6.0. It only completed hippocampal segmentation for the left hemisphere, but not the right. Under scripts folder, recon-all.error says: /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/recon-all PWD /ifs/scratch/pimri/posnerlab/1anal/osa/fs2/B03/label CMD /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/segmentSF_T1.sh /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/MCRv80 /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer B03 /ifs/scratch/pimri/posnerlab/1anal/osa/fs2 left So it seems as left hippocampus failed the pipeline didn’t try the right hippocampus. Attached is hippocampal-subfields-T1.log. Do you have any idea what’s happening here? Best, Jiook

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Centroid of a binary volume question
by pfotiad＠nmr.mgh.harvard.edu 22 Jan '16

22 Jan '16

Dear FS Community, I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help! Best, Panos

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LME results - Talairach coordinate, surface area
by Hanbyul Cho 22 Jan '16

22 Jan '16

Dear FreeSurfer Team, I am wondering how I can report Talairach coordinate and cluster size (=surface area, mm^2) of the LME corrected results. We can count the each clusters' number of vertices on fsaverage template by checking the *.label. (is it right?) However, I don't know how we can the clusters' talairach coordinate and the cluster size of LME results. This results form differed from GLM results form of Freesurfer. Could you let me know the method of calculation the clusters coordinate and size after LME analysis by LME MATLAB tool? Best Regards, Han.

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(no subject)
by Erik Lindberg 22 Jan '16

22 Jan '16

I just want to investigate significant correlation with the csf variable correcting for apoe-status, gender, diagnosis and age below previous correspondence your classes are right. What are you trying to test with your contrast matrix? On 01/20/2016 05:33 AM, Erik Lindberg wrote: > Dear Freesurfers, > > I am running a design in which I want to correct for a number of > categorical variables: diagnosis, gender and apoe status and one > continuous variable (age) in a correlation analysis > > Did I get this right? (below) > > Thanks, Eric > > GroupDescriptorFile 1 > > Title MyTitle > > Class AMCI_F_APOE- > > Class AMCI_F_APOE+ > > Class AMCI_MALE_APOE- > > Class AMCI_MALE_APOE+ > > Class CTL_FEMALE_APOE- > > Class CTL_FEMALE_APOE+ > > Class CTL_MALE_APOE- > > Class CTL_MALE_APOE+ > > Class NON_A_MCI_FEMALE_APOE- > > Class NON_A_MCI_FEMALE_APOE+ > > Class NON_A_MCI_MALE_APOE- > > Class NON_A_MCI_MALE_APOE+ > > Class SCI_FEMALE_APOE- > > Class SCI_FEMALE_APOE+ > > Class SCI_MALE_APOE- > > Class SCI_MALE_APOE+ > > Variables AGE_DEMEAN CSF_Ab40_ADx > > > With the contrast matrix: corr.mtx: > > 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 > 1 1 1 1 1 1 1 1 1 1 1 1 1 > > > > _______________

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(no subject)
by Erik Lindberg 22 Jan '16

22 Jan '16

I just want to run plane correlation with the csf-variable best Eric

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