Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Subcortical Label
by Kelly Silva 08 Jan '09

08 Jan '09

Hello, I´d like to know if there is some way to create a ROI-label of a subcortical structure. If there is a way, please tell me how to do. Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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mri_vol2surf - MNI subject
by Yigal Agam 08 Jan '09

08 Jan '09

Hi, If I have volume data in MNI subject space (produced using --tal option in mri_vol2vol), how do I project it onto the surface in the same subject space? There does not seem to be an equivalent tal option in mri_vol2surf. Thanks, Yigal

1 0

Trouble Creating label
by Zeidan, Mohamed A. 07 Jan '09

07 Jan '09

Hello all, I'm creating a label on a volume in tkmedit and as I do it, tkmedit will unexpectedly close and give me the following error message in the terminal window: =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to analysis-bugs(a)nmr.mgh.harvard.edu : : Now exiting... Any thoughts? Thanks, Moe

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Averaging two SPGR
by antonio cerasa 07 Jan '09

07 Jan '09

Dear List Does anyone know how to get more detailed information on the specifics of the method used to average two SPGR (or MPRAGE) sequences ? -------------------------------------------------------------------------- Antonio Cerasa PhD Laboratory of Neuroimaging Institute of Neurological Sciences National Research Council (CNR) Cosenza, Italy.

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Parameter comparison in native vs. template space
by Christine Ecker 06 Jan '09

06 Jan '09

I would like to export cortical thickness measures and compare the data across subjects in a vertex-by-vertex fashion. Please could you confirm that similar functions such as mri_glmfit are based on the parameters in template space e.g. lh.thickness.fsaverage.mgh and not on the parameters in native space e.g. lh.thickness. So for a group comparison I would have to export the files in template space (e.g. lh.thickness.fsaverage.mgh) and could then map the output back onto the template? Also, why are the parameters not the same in native and template space? Finally, in order to compare groups on the basis of the parcellated regions (e.g. lh.aparc.stats). Are parameters such as area, volume, curvature etc comparable across groups or would they still have to be corrected for whole-brain volume? I would be very grateful if you could help me further. Thank you!

2 1

Loading Projects Files
by Bramen, Jennifer E. 06 Jan '09

06 Jan '09

Dear Freesurfer Community I have been unable to load any of my saved Project files , and I cannot find any explanation in the tutorial or in the list arcives. I have been saving the project files inside of the qdec/<Design Name> directory as <?h_description>.qdec. However, when I try to load them, I get an error. I am using Qdec 1.1. Any ideas about what is wrong? Thank you. Best regards -- Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 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.

2 1

How to overlap FSL statistical map onto surface in Matlab?
by Yunjie Tong 06 Jan '09

06 Jan '09

Hi I was able to view the statistical maps (from FSL) on the subject's surface following the tutorial (FsTutotial/FSLFeatFreeSurfer). I would like to see the same image in Matlab. I could show the subject's surface as well as the the cortical parcellation in Matlab by modifying the functions freesurfer_read_surf.m and read_annotation.m. I do not know how to overlap the statistical map onto the surface then. Is there any Matlab function I can use? Thanks. Best, Yunjie

2 3

Poor labeling
by Jason S. Minamora 06 Jan '09

06 Jan '09

Hello, I'm using a home-grown GCA constructed from five acallosal subjects to try to improve the automatic labeling and segmentation of volumes from this population. However, the labeling was quite bad when performed on a representative subject, and the ventricles were only partially filled and crossed the IHF in areas: Left_Lateral_Ventricle (4): linear fit = 1.00x + 0.0 (713 voxels, overlap=0.480) Left_Lateral_Ventricle (4): linear fit = 1.00x + 0.0 (713 voxels, peak = 38), gca=37.8 Right_Lateral_Ventricle (43): linear fit = 1.00x + 0.0 (370 voxels, overlap=0.292) Right_Lateral_Ventricle (43): linear fit = 1.00x + 0.0 (370 voxels, peak=38) I also noticed that the 152-subject MNI atlas that came with FS had ventricles that were much "darker" (when converted to NIFTI and displayed in fslview) than my own atlas: the mean ventricle intensities were about 15 and 30, respectively. We suffer from a lack of data, too. Is it possible to improve the GCA and labeling with such limited data? Jason

2 1

Problem with post-spm registered data
by Dave Brohawn 06 Jan '09

06 Jan '09

Hello, Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in tkmedit seemed to be shifted inferiorly in the coronal view by a wide margin (an inch or so), leaving no functional activation in the top of the cortex, even when set at an extremely low threshold. When running the fMRI scan, we checked our slice prescription and ensured the area of view covered the entire cortex. We also checked the raw data output during the scan in the viewing window, and functional activity was present. After running the unpacking and recon-all processes, I ran the pre-proc command and spm-register, and viewed the output using tkregister2. The registered functional data matched up beautifully with the underlying anatomy, and went right to the top of the cortex in the coronal view. We ran our analysis using the appropriate paradigm files (has worked without fail for our previous subjects) and there is no functional activity in the top inch or so of the cortex whatsoever. Please let me know if you have an answer to how this could have happened. Dave Brohawn

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reg-feat2anat failed
by Wang, Xin 06 Jan '09

06 Jan '09

Hello, Freesurfer group, I am registering the fMRI results to surface using reg-feat2anat (v 1.26.2.1 2007/08/15) and tkregister2. The automatic registration catastrophically failed in the subject space, but worked fine in the standard space. The orientations of example_func.nii.gz in the subject space are flipped in any view. I use the tkmedit to view the example_func, and found the orientation is wrong. It seems Freesurfer can not read nifti header correctly. I attach the reg-feat2anat log file and an example_func.nii.gz. I found the following message from Freesurfer email list. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html Does Freesurfer have a solution for this type of problems by now? Thank you in advance, Xin

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