Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

problem with nu_correct
by Andrea Tateo 24 Jul '13

24 Jul '13

Hi FreeSurfer expert, I have a problem with command "recon-all". In recon-all.log I can to read nu_correct: crashed while running nu_evaluate (termination status=9) Thank for your help

2 1

bvecs error from Tracula
by amirhossein manzouri 24 Jul '13

24 Jul '13

Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri

3 12

mri_label2label "ERROR: srcvtxno=-1"
by Lingqiang Kong 24 Jul '13

24 Jul '13

Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###---------------------### Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###---------------------### The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine. Did anyone have this problem before or know how to resolve this? Thank you. BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.… in the archive but it was never followed up. Lingqiang -- Lingqiang Kong Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/

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how to threshold mgh surface and save the file
by Robert Schulz 24 Jul '13

24 Jul '13

Hi, I'd like to theshold a surface mgh file at a certain value, set all values below the threshold 0 and save the file for further statistical analysis. mri_binarize creates a binary mask which does not help in my case. Could anybody help me with the apprpriate command? Thank you very much Best wishes, Robert -- Besuchen Sie uns auf: www.uke.de _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Astrid Lurati (komm.), Joachim Prölß, Matthias Waldmann (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

2 1

mri_convert errors
by Pom Sailasuta 24 Jul '13

24 Jul '13

Hello, I have several errors using mri_convert to convert 3T Philips T1-wt, DTI and fMRI images. The last one on T1-wt images tells me to send email to freesurfer, so here is the error messages: [pom@PomLinux /home/pom]% !mri mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from IM_0001... Starting DICOMRead2() dcmfile = /home/pom/Software/freesurfer/subjects/S009002A/mri/orig/orig2/IM_0001 dcmdir = /home/pom/Software/freesurfer/subjects/S009002A/mri/orig/orig2 WARNING: tag image orientation not found Ref Series No = 2 ERROR: bits = 8 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu for DTI images, here is the errors: MRIalloc(0, 0, 1855): bad parm [pom@PomLinux /home/pom]% mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from IM_0001... Starting DICOMRead2() dcmfile = /home/pom/Software/freesurfer/subjects/S009002A/mri/orig/IM_0001 dcmdir = /home/pom/Software/freesurfer/subjects/S009002A/mri/orig Ref Series No = 501 Found 1874 files, checking for dicoms WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found Found 1855 dicom files in series. WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag image orientation not found WARNING: tag SeriesNumber not found WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: -117.09 -112.869 17.456 Vs: -0.715854 -0.690047 0.106721 Second Sorting Counting frames nframes = 1 nslices = 1855 ndcmfiles = 1855 MRIalloc(0, 0, 1855): bad parm ERROR: mri alloc failed I would greatly appreciate any help. thanks so much Pom

1 0

MNI coordinates
by LAOUCHEDI MAKHLOUF 23 Jul '13

23 Jul '13

Hi i am using corticals parcels (destrieux) as nodes in a connectivity study using the NBS (Network Based Statistics) tool; i want to assign MNI coordinates for these nodes. is there any MNI coordinates in freesurfer for each component of this parcellation (not for every vertex in those components) or any other strategy to assign coordinates for these components ? otherwise, i intend to non-linearily register the freesurfer's labels for a healthy subject in MNI and for each label i will use coordinates of one of its points to represent that label thanks for help

2 1

help needed with fsgd file and contrast matrix for correlation analysis
by Robert Schulz 23 Jul '13

23 Jul '13

Dear all, I have 2 short questions regarding a correlation analysis I'd like to perform with mri_glmfit (surface-based DTI data are correctly preprocessed and concatenated into mgh file, statistics are performed on fsaverage space). 1) I'd like to look for correlation between the surface-data and a behavioural measure BEH in one group, correcting for gender and age. I set up the following fsgd: GroupDescriptorFile 1 Class Male Class Female Variables BEH Age Input subj1 Male 0.76 72 Input subj2 Male 0.44 67 Input subj3 Female 0.33 80 .... My contrast file is: 0 0 0.5 0.5 0 0 (referring to the FSGD examples Fsgd2G2V, GLM with 2*(2+1) columns). Is this setup correct? If not, how would I have to set up fsgd and C? 2) In a next step, I'd like to answer the question (now including another group2): Where does group1 (OLD) show increased correlation with BEH compared to group2 (YOUNG), correcting for GENDER and AGE within each group. I wonder because AGE is the relevant difference between both groups. GroupDescriptorFile 1 Class OldMale Class OldFemale Class YoungMale Class YoungFemale Variables BEH Age Input subj1 OldMale 0.76 72 Input subj2 OldMale 0.44 67 Input subj3 OldFemale 0.33 80 .... Input subj11 YoungMale 0.80 20 Input subj12 YoungMale 0.55 21 Input subj13 YoungFemale 0.44 31 .... My contrast file would look like: 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 (referring to GLM with 4*(2+1) columns). Correct? Thank you very much for your help! I am really not sure whether I did it correctly and whether I can trust my results. Best wishes, Robert -- Besuchen Sie uns auf: www.uke.de _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Astrid Lurati (komm.), Joachim Prölß, Matthias Waldmann (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

2 1

issue with mri_label2vol
by Cesar Echavarria 23 Jul '13

23 Jul '13

Hello freesurfers I want to convert a surface-defined label to an auxiliary volume file. I've created my label on the right hemisphere. I then enter the following command to convert this label into a volume mri_label2vol --label /cluster/tootell/pitcairn/1/users/Cesar/good_subjects_anat/abir_anat/label/Retinotopy/RH_V1horizontal.label --temp /cluster/tootell/pitcairn/1/shahin/good_subjects_anat/abir_anat/mri/orig.mgz --regheader /cluster/tootell/pitcairn/1/shahin/good_subjects_anat/abir_anat/mri/orig.mgz --subject abir_anat --hemi rh --proj frac 0 1 .1 --o /cluster/tootell/pitcairn/1/users/Cesar/good_subjects_anat/abir_anat/mri/RH_V1horizontal.mgz When I load the auxiliary volume file into tkmedit, I find that the volume is actually on the* left* hemisphere. I would appreciate any help pointing out where my commands/ my thinking went wrong. Let me know if images would be helpful Thanks, Cesar Echavarria

2 1

inflate surface until sphere
by Lo, Yiping 23 Jul '13

23 Jul '13

Hi Freesurfer, I am tring to inflate pial surface until the sphere. I have tried mris_inflate and set the number of iteration to be large. However, it seems to inflate the brain to a limit and no further inflation. I have also tried mris_sphere, but it seems not what I want. It more likely to map the pial surface onto a sphere and inflate it along the sphere. I should say in advance, I only got .pial file. What should I do to get what I want? Best Wishes, Yi-Ping DISCLAIMER: This email is intended solely for the addressee. It may contain private and confidential information. If you are not the intended addressee, please take no action based on it nor show a copy to anyone. In this case, please reply to this email to highlight the error. Opinions and information in this email that do not relate to the official business of Nottingham Trent University shall be understood as neither given nor endorsed by the University. Nottingham Trent University has taken steps to ensure that this email and any attachments are virus-free, but we do advise that the recipient should check that the email and its attachments are actually virus free. This is in keeping with good computing practice.

2 1

help needed with fsgd file and contrast matrix for correlation analysis
by Robert Schulz 23 Jul '13

23 Jul '13

Dear all, I have 2 short questions regarding a correlation analysis I'd like to perform with mri_glmfit (surface-based DTI data are correctly preprocessed and concatenated into mgh file, statistics are performed on fsaverage space). 1) I'd like to look for correlation between the surface-data and a behavioural measure BEH in one group, correcting for gender and age. I set up the following fsgd: GroupDescriptorFile 1 Class Male Class Female Variables BEH Age Input subj1 Male 0.76 72 Input subj2 Male 0.44 67 Input subj3 Female 0.33 80 .... My contrast file is: 0 0 0.5 0.5 0 0 (referring to the FSGD examples Fsgd2G2V, GLM with 2*(2+1) columns). Is this setup correct? If not, how would I have to set up fsgd and C? 2) In a next step, I'd like to answer the question (now including another group2): Where does group1 (OLD) show increased correlation with BEH compared to group2 (YOUNG), correcting for GENDER and AGE within each group. I wonder because AGE is the relevant difference between both groups. GroupDescriptorFile 1 Class OldMale Class OldFemale Class YoungMale Class YoungFemale Variables BEH Age Input subj1 OldMale 0.76 72 Input subj2 OldMale 0.44 67 Input subj3 OldFemale 0.33 80 .... Input subj11 YoungMale 0.80 20 Input subj12 YoungMale 0.55 21 Input subj13 YoungFemale 0.44 31 .... My contrast file would look like: 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 (referring to GLM with 4*(2+1) columns). Correct? Thank you very much for your help! I am really not sure whether I did it correctly and whether I can trust my results. -- Besuchen Sie uns auf: www.uke.de _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Astrid Lurati (komm.), Joachim Prölß, Matthias Waldmann (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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Freesurfer July 2013