Freesurfer

freesurfer@nmr.mgh.harvard.edu

9 participants
30092 discussions

Converting Surface Masks to Labels
by Rita Loiotile 15 Feb '17

15 Feb '17

Hi, I'm sorry for what seems like a trivial question. I couldn't find this answer in the tutorials or old archive. I have statistical data in the surface that I have thresholded and binarized to form a mask. I can load the mask as an overlay in tksurfer. My understanding is that you need to turn files into labels in order to change the color display in tksurfer. Is there a command that takes in a shape/surface binary file and converts to labels? I came across this (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-March/017668.ht…) email from Doug, but it looks like I don't have mri_seg2annot in this freesurfer release. More broadly, I would like to tksurfer to display several masks at once, in different colors, using the command line. My understanding is that I would then use mris_label2annot to put all the labels together. When using this function, does the input order of the labels determine the number reference for the color in the Lookup table? What happens in the case where some labels overlap? Thank you in advance, Rita

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bbregister
by John Anderson 15 Feb '17

15 Feb '17

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Coordinates in different modality and space
by Ting Qi 15 Feb '17

15 Feb '17

Dear freesurfer experts, I have some questions about the coordinates conversion, and the relationship between several types of coordinates. First of all, I’d like to confirm whether the coordinates reported in the results summary are based on MNI305 space? Second, I plan to combine multi-modalities data, therefore I would like to use the peak vertex in the surface as a seed to do additional volume-based analysis. I have the vertex index, vertex ras, MNI coordinates reported in the summary text, but how can I get the correct and corresponding volume coordinates in MNI space, particularly in MNI152? I read the page about the freesurfer coordinate system, they mentioned several cases about the transformation, but I still cant figure out what is the correct way in my case. Moreover, I tried the mni305 to mni152, but when I double checked the coordinates in mni152 space, the peak was no longer corresponds to the region reported in the mni305 space. So I sure there must be something wrong. Finally, would anyone offer me a explanation about the relationship between surface RAS, volume RAS, MNI* RAS, Vertex MNI, Volume MNI coordinates? It quite confused me. Thanks in advance, Best regards, Ting

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Normalization of external regressors
by Reza Rajimehr 15 Feb '17

15 Feb '17

In a functional analysis, we have a set of external regressors (e.g. mean luminance of stimuli, size of stimuli, etc.). Should we normalize values before including them in the regressor files? If so, what is the recommended way of normalization ... z-scoring? Thanks, Reza

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PET ROI analysis
by Donatas Sederevicius 15 Feb '17

15 Feb '17

?Hello FreeSurfer Developers, I have done partial volume correction of PET data as described in PETSurfer stream. Now, I want to extract a mean intensity value of my ROI for each subject. This ROI is defined in the fsaverage space and saved as a label. What would be the best way to do it? Should I start from mri_label2label command to map the label to the individual anatomical space or there is another, maybe easier way to do it? Thanks in advance. -Donatas

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Freesurfer v6.0 / Developer version GPU implementation
by Francis Tyson Thomas 15 Feb '17

15 Feb '17

Hi, I'm trying to reduce the freesurfer runtime as much as possible and I was wondering if the GPU flags still work for recon-all in Freesurfer v6? If not is it possible to use the developer version to have it running? Also, if I follow the second approach would the results be the same as that obtained through CPU implementation? Thanks, Tyson

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Intensity Re-scaling Relative to Full Brain Atlas <Repost>
by Anderson Napolitano 15 Feb '17

15 Feb '17

Hi Experts! Quick question: is it possible to re-scale intensities relative to the full brain atlas? Details: Per step 3 of the following tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer I wanted to re-scale the the intensities relative to the full brain atlas. The command: --no-rescale removes scaling relative to the Pons and the command: --rescale <Ids> rescales the intensities relative to the region determined by Ids. Would listing all the regions on the --rescale command be the right approach to rescale the intensities relative to the atlas? If so, how do I determine which Ids is which? Thank you in advance! -Anderson

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surface based PET analysis.
by miracle ozzoude 15 Feb '17

15 Feb '17

Hello Freesurfer, I want to perform surface based PET analysis but I can't seem to find a link for it. Please can someone direct it to me. Thanks. Best, Paul

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FS6.0, recon-all -parallel on OSX Sierra, dyld: Symbol not found: ___emutls_get_address
by Mira Michelle Raman 15 Feb '17

15 Feb '17

Good morning, I get the following error when running recon-all -all -parallel on my OSX Sierra (10.12.1) iMac (Note: the same subject completes w/o error when NOT using the -parallel flag) dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib I am attaching both the /usr/lib/libSystem.B.dylib file from my computer along with the subject's recon-all.log file. My system: Late 2012 iMac with an i7 processor, 24GB RAM, running OSX 10.12. Sincerely, Mira _______________________________________________ Mira Michelle Raman Lead Scientific Programmer The Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd, Ste. 1356

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recon-all when the input is the brain
by Li,Tengfei 15 Feb '17

15 Feb '17

Hello, If my input file of Freesurfer is the exacted brain.nii instead of T1 image T1.nii, how should I run recon-all? The brain has already been extracted and skull has been stripped by other softwares. Shall I run like the following: recon-all -noskullstrip -normneck -autorecon-all -subjid ID (or -noskull-lta) ? Thanks. -Tengfei The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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