Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Registering scans with different voxel sizes/numbers
by zalewk＠u.washington.edu 05 Jul '16

05 Jul '16

Hello Freesurfer team, I have the unfortunate task of performing longitudinal volumetric analysis on subjects collected on three different scanners with different voxel numbers/sizes. I didn't find this out until attempting to run the longitudinal base and receiving this message: WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. By re-registering the original nifti and recreating the norm.mgz/talairach I can correct the geometry, but FSL's Flirt will only work with niftis and not mgz volumes, ergo I can't re-register the manually edited brainmask/wm volumes properly. I was wondering if there were any freesurfer tools I could use to simply re-register the .mgz volumes to the new norm.mgz? If so, how would I go about doing that? Seeing as the brainmask/wm are both registered to 256^3/1mm anyhow, is this something I should even be concerned about? Thanks, KZ

2 3

retinotopic analysis
by Francesca Strappini 05 Jul '16

05 Jul '16

Hello Freesurfers, Where can I find any documentation about how is retinotopic analysis performed in Freesurfer? Thanks. Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

1 0

Maps/seed on surafce
by Martin Juneja 05 Jul '16

05 Jul '16

Dear FreeSurfer and SPM experts, I am trying to calculate functional connectivity maps using FreeSurfer pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… . After defining a seed region on raw anatomical image, I co-registered functional data with anatomical data (as reference) and made sure that the seed is at correct place on both anatomical (top left in attached image) and functional (top right) data. Using SPM, I confirmed co-registration was fine. But after running all the steps of FC, looks like the FC maps are not correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I am not getting significant FC at seed location. Here, bottom right shows the seed location on surface after I convert the seed to fsaverage space (for visualization purpose). Any thoughts, ideas or tips on what went wrong here, would be really appreciated. Thanks.

2 3

Hippocampus & Amygdala Volume Accuracy
by Limachia, Gaurang (NIH/NINDS) [F] 05 Jul '16

05 Jul '16

Hello Bruce, I am uploading the data set to filedrop for you to look over. Can you assist us in determining the optimal method for parcellation of the white and gray matter. We are particularly interested in determining the volume of the hippocampus and amygdala. Are there any special parameters we should use for these structures? Therefore, we want to improve the accuracy of the pial and white matter surfaces. I would greatly appreciate your help. Best Regards, Shyam

1 0

retinotopy analysis documentation
by Francesca Strappini 05 Jul '16

05 Jul '16

Hello Freesurfers, I'm re-posting this question. Where can I find any documentation about how is the retinotopic analysis performed in Freesurfer? Thanks. Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

1 0

Order of overlays
by Reza Rajimehr 05 Jul '16

05 Jul '16

Hi, In Tksurfer, we want to show functional activity map and borders of aparc on a surface. The borders of aparc are always drawn on top of the activity map, which sometimes hide small activation blobs. Is it possible to draw the activity map on top of the aparc borders? Reza

5 4

[TRACULA] ERROR: cannot unpack mosiacs without ASCII header
by Koubiyr, Ismail 05 Jul '16

05 Jul '16

Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail

2 10

Fwd: Failure to use yeo-7/17 networks maps as templates in MRIcron
by Hsiang-Yuan Lin 04 Jul '16

04 Jul '16

Hi Prof. Yeo, I have problems utilizing yeo 7/17 cortical network parcellation maps as templates in MRIcron (I aim to use your cortical parcellation maps to underlay my findings in order to derive the implications based on iFC networks). To be specific, there is an orientation problem in the current version of parcellation maps in MNI space. Thank you for your help in advance. Best, Hsiang-Yuan -- *Hsiang-Yuan Lin, M.D.* *Attending Psychiatrist & Adjunct LecturerDepartment of Psychiatry & Child Mental Health CenterNational Taiwan University Hospital and College of Medicine* email: louislin28(a)gmail.com CV: https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=shari… <https://drive.google.com/file/d/0B3jQGSXih2aeX0tGbXM2d2Rkd0E/view?usp=shari…> https://www.researchgate.net/profile/Hsiang_Yuan_Lin2 -- *Hsiang-Yuan Lin, M.D.* *Attending Psychiatrist & Adjunct LecturerDepartment of Psychiatry & Child Mental Health CenterNational Taiwan University Hospital and College of Medicine* email: louislin28(a)gmail.com CV: https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=shari… <https://drive.google.com/file/d/0B3jQGSXih2aeX0tGbXM2d2Rkd0E/view?usp=shari…> https://www.researchgate.net/profile/Hsiang_Yuan_Lin2

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Re: [Freesurfer] controlling for total gray matter volume (Clara K?hn)
by Arkadiy Maksimovskiy 04 Jul '16

04 Jul '16

Hi Clara, Yes- my apologies. I misunderstood your initial analyses description. Sounds right to me as well. - Arkadiy

2 1

Re: [Freesurfer] longitudinal tracula
by Harms, Michael 04 Jul '16

04 Jul '16

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