Freesurfer

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17 participants
30099 discussions

LGI in Qdec
by krista kelly 05 Mar '14

05 Mar '14

Hello, I followed instructions on how to incorporate the lgi_pial measure into QDec, however, it's not coming up when I go to choose this as a measure. I ran recon-all -s my_subject_id -qcache -measure pial_lgi and created a Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any insight as to why this may be occurring? Thanks, Krista

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Qdec failed
by Yinfei Li 05 Mar '14

05 Mar '14

Dear experts, I have Freesurfer running quite well on Ubuntu for some time. But today when I tried to run the command ‘qdec’, I got the following error: Qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory How do I fix this? Thank you. Yinfei

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different thickness after converting wm.mgz in nifti and back
by Koschutnig, Karl (karl.koschutnig＠uni-graz.at) 05 Mar '14

05 Mar '14

Dear experts, our group decided to make all the white matter edits in brainvoyager (don't ask me why;-). So we converted the wm.mgz into nii and then into the brainvoyager format vmr, made the edits and the same way back into freesurfer. We started the recon-all -autorecon2-wm … and found massive reduction in the thickness. So far so bad. To figure out the problem we started at the beginning of the conversion-mess and converted the wm.mgz into wm.nii and back into wm.mgz and found nearly the same reduction in the thickness. Finally, here comes my question. Is it possible that due to interpolation errors in the mri_convert routine this reduction can be explained? PS: here is the output from mri_diff for the wm_orig.mgz and the converted one: Volumes differ in geometry row=1 col=1 diff=0.000000 (5.96046e-08) Please fin attached the reconstructed white matter surface (red = original, yellow = after converting the wm from nii in mgz and back) thank you so much best Karl

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Is there a better direction for acquiring T1 structural scan? sagittal or axial
by Tartaglia, Carmela 05 Mar '14

05 Mar '14

I am wondering if there is a preferred direction for acquiring T1 structural scan? sagittal or axial? and what is the rational? Thanks Carmela This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

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Combining sagittal and axial T1 for volumetric analysis
by Tartaglia, Carmela 05 Mar '14

05 Mar '14

I have patients and controls scanned on the same scanner but their data was acquired in different orientations. One group is sagittal and the other is axial. The sizes are 1X1X1 vs 1X1X1.2. Is it possible to combine these images for freesurfer analysis? Thanks carmela This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

2 1

comparing models
by Eric Cunningham 04 Mar '14

04 Mar '14

Hello Freesurfer experts, I have a question about how to determine if a covariate is important in a mixed effects model for example: Y1 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) + B5(covariate_1) +B6(covariate_2) Y2 = B1 + B2(time) + B3(rand_effect1) + B4(rand_effect*time) + B5(covariate_1) Would it be appropriate to use the lme_mass_LR script? (the script says it is for comparing models with q and q+1 random effects). Thanks, -E

2 2

Temporal horn measures
by Rashmi Singh 04 Mar '14

04 Mar '14

Is there any way to get the volume for the temporal horn using FreeSurfer. Thanks, Rashmi

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QDEC bad fd number
by Mihaela Stefan 04 Mar '14

04 Mar '14

Hi freesurfers, I get this error when I load qdec.table.dat. Is it something wrong or should I ignore it? Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '6027' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '6209' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '6243' in SUBJECTS_DIR . . . ERROR: QdecProject::VerifySubjects: Couldn't find subject '6052' in SUBJECTS_DIR Too many subjects not found! Someone else complained about the same problem but there was no reply: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08288.html My qdec.table looks like this: fsid diagnosis Cage 6027 ABN -1.39 6209 ABN 2.61 . . Thanks! Mihaela

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Add new path to tracula
by Francesco Baldacchini 04 Mar '14

04 Mar '14

Hi everybody, I'd like to know if it's possible and if yes how to add new paths to the tracula pathlist? Otherwise how can I add a new path after the entire trac-all process? Francesco Baldacchini

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Compute DTI metrics in NAWM in Tracula
by Celine Louapre 04 Mar '14

04 Mar '14

Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine -- Celine Louapre, MD-PhD, Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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