Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Freesurfer/Freeview Version Compatibility
by Edwards, Vincent 01 Jan '24

01 Jan '24

External Email - Use Caution Hi, I'm following up on my quick question from this time last week. I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point edits, would I be able to do recon-all through Freesurfer 7? Years ago, someone asked if they could do recon-all in an older version of Freesurfer and edit in a newer GUI. Doug said that was fine. My question is basically the inverse of their problem. I assumed that since Freeview is a GUI, the version used shouldn't have any actual impact on things as long as we returned to version 7 to recon-all. I just want to confirm that my assumption is correct? The pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 (recon-all for pial/wm/cp's) Thanks, Vincent Edwards

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Statistical Characteristics of Segmented Fornix from T1-w MR Images
by Ahsan Ali 01 Jan '24

01 Jan '24

External Email - Use Caution Dear Sir/Madam, I have segmented T1-W MR images from the ADNI database using Freesurfer. From aseg.nii, I have estimated the fornix structure (label number 250). I tried many times to get the characteristics of these structures but couldn't. It would be helpful for me; kindly let me know. File name "fornix.nii" at label 250. Its statistical parameters, such as fractal dimension, volume, mean, etc With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552

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Case-controls study !
by Martin Juneja 01 Jan '24

01 Jan '24

External Email - Use Caution Hello FreeSurfer experts, In my case-control study, I have a dataset of 5 healthy controls (HCs) and one patient (PAT). I was wondering if there is any way to perform GLM for PAT > HCs on brain morphometry data. When I tried to follow instructions from here: https://secure-web.cisco.com/1og9s8_rd4Lyx1NIwR7d0GRha020qNYi0MbIToxO7mZZ68…, the mri_glm fit command gives me the following error: Class Size and Means of each Continuous Variable 1 HC 5 24.2000 0.6000 2 Tumor 1 50.0000 1.0000 ERROR: Class Tumor has 1 members. With 2 variables and using DODS, you need at least 3 members It seems at-least three subjects are required in the Tumor category - because I have age and sex covariates in my fsgd file. I was wondering if there is any way to still perform the above GLM analysis or any other alternatives available to compare HCs vs one PAT. Thanks!

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mri_cc question
by Dawn Matthews 01 Jan '24

01 Jan '24

External Email - Use Caution Hello Freesurfer team and thank you for your continued responses to questions. My questions pertain to mri_cc, and subsegmentation of the corpus callosum. In prior runs of version 6.0, it seems that aseg outputs the subregions of the corpus callosum. The option for mri_cc also identifies those segments, and (Question 1) I wondered if in version 7.4 how that differs from what aseg normally outputs? In addition, (Question 2) with the -f flag to include the fornix, does this mean that the fornix is incorporated into the five subvolumes, or is the fornix volume calculated separately? (Question 3), For the option to set a different number of segmentations, how does that translate into the five ‘default’ segments (e.g. Anterior, Mid-Anterior, Central, Mid-Posterior, Posterior). Again, thank you for the team’s continued work.

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Freesurfer/Freeview Version Compatibility
by Edwards, Vincent 01 Jan '24

01 Jan '24

External Email - Use Caution Hello, I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point edits, would I be able to do recon-all through Freesurfer 7? I assumed that since Freeview is a GUI, the version used shouldn't have any actual impact on things as long as we returned to version 7 to recon-all. That seemed to be the case when someone asked a similar question (the reverse) <https://secure-web.cisco.com/1T0BQhB8dtRKrnTUmjN8XbkGqwEO9_yqoJso_TElGy705p…> , but that was many years ago so I wanted to confirm. Thanks, Vincent Edwards

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FW: Boundary based registration
by Spapens, Jeltje (NP) 01 Jan '24

01 Jan '24

External Email - Use Caution Hello Freesurfer developers, I want to register an MRI slap to a full FoV UNI scan of the same subject, but I get a false reorientation with my code (see attached image). I have tried multiple input and tried the script on different subjects. I also changed som flags such as -init-header and --cubic, but all seem to give the same results. bbregister --s MRS_200_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --t2 --init-fsl mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_acpc_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_regt1.nii.gz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat –trilin I would appreciate to hear your thoughts on this problem. Have a nice weekend and kind regards, Jeltje Spapens

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Use pial or white surface area of FreeSurfer?
by free_learner 01 Jan '24

01 Jan '24

External Email - Use Caution Dear experts, Surface area is a commonly used metric. Unlike thickness and volume, area could be calculated based on white surface or pial surface in FreeSurfer. I don’t know which one should be better used for analysis. I believe the pial surface area is more sensitive to brain changes such as gray matter atrophy. But the white surface area is the default in FreeSurfer and thus probably the one used in papers. Maybe I should use the mean area of white and pial surface? Best, Yang Hu

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Tksurfer option for horizontal scale bar
by Lee, Jeungchan 01 Jan '24

01 Jan '24

Hi Freesurfers, I’m using TkSurfer to visualize my results and want to add a horizontal color scale bar. I used [ -colorscalebarflag 1 ] to do so, but I only got a vertical bar. Is there any way (command options) to get a horizontal color scale bar? Thanks, jeungchan

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Brainnetome atlas
by Blanca Zufiria Gerbolés 01 Jan '24

01 Jan '24

External Email - Use Caution Dear all, I would like to extract the cortical thickness, subcortical volumes and eTIV from the Brainnetome atlas of subjects I have preprocessed with FreeSurfer v7.3. I understand this entails several steps. Could someone advise me how to do this? Best wishes, Blanca När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://secure-web.cisco.com/1UfjSvkpcEA-W18RIWXnAOlIhR9tz8hfZlA7NdpYFKSpWW…>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://secure-web.cisco.com/1VCHcReN3VOjcjz8kTVUawgcRo_JbylQUb1S4aWfBcPzFl…>.

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Help with transform matrix for SEEG
by Hyunchul Lee 01 Jan '24

01 Jan '24

External Email - Use Caution Hello, I've just started using Freesurfer this week and I'm quite confused about coordinate systems. Specifically, I have SEEG electrode locations that have been digitized in MRI RAS space, and I'm trying to apply a transform matrix so that these electrodes will be registered with the same brain that I performed recon-all on using Freesurfer, so that I can do further analysis in MNE python. I understand that voxel space to MRI RAS space transform matrix is stored in vox2ras and the transform for voxel space to Freesurfer's surface RAS is in vox2ras_tkr of T1.mgz in my subject folder. Since the electrodes are in MRI RAS space, I am applying a transform matrix that is a matrix product of inverse(vox2ras) and vox2ras_tkr. However, this doesn't work out in real life, and I end up with electrodes half way outside the head. Am I using the correct matrices? Also, T1.affine appears similar to vox2ras but very slightly different. Just hoping that there would be an easier way.. Best regards, *Hyunchul Lee* MBBS PhD

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