[Freesurfer] A Help Request for Freesurfer Installing

External Email - Use Caution Hello; This is Maedeh Khalilian, a master student at Shiraz University of Technology. I have ubuntu 18.04 LTS installed on my laptop. I have already installed Freesurfer package but it is the version for CentOS. I wonder if I can use it with ubuntu

[Freesurfer] (no subject)

External Email - Use Caution Dear FreeSurfer experts, I would like to use the FreeSurfer package to do a parcellation.Just for testing, I am using "buckner_data" and there is a step I have been stuck in.I have problem using "mris_ca_train" command.This is the whole code I run

[Freesurfer] The Problem Using "mris_ca_train"

External Email - Use Caution Dear FreeSurfer experts, I would like to use the FreeSurfer package to do a parcellation.Just for testing, I am using "buckner_data" and there is a step I have been stuck in.I have problem using "mris_ca_train" command.This is the whole code I run

[Freesurfer] A Question about mris_divide_parcellation

External Email - Use Caution Dear experts; By using "recon-all", I have parcellated an MR image and by using "mris_divide_parcellation" i have subdivided the result into specific regions,(each region has been divided into 10 subregions), the question I have is that are these sub

[Freesurfer] "A question about mris_divide_parcellation"

External Email - Use Caution Dear Dr.Bruce Fischl Thx for replying. You told me that inequality of the subregions depends on the code I ran. First off I ran the command: recon-all -subject test -i data_00.nii -all "data_00.nii" is a raw MR image. Then, I ran this command: mris

[Freesurfer] A Help Request for Random Parcellation

External Email - Use Caution Dear Dr.Bruce Fischle; Thank you very much for all help you have given me so far,I would like to know if it is possible to access the algorithms(or any specific parts of them) that run FreeSurfer and I also would like to know if I can do a random pa

[Freesurfer] Seeing the Parcels as Volumes

External Email - Use Caution Dear FreeSurfer experts, I have used "mri_annnotation2label" and "mri_label2vol" to change the parcellation output of FreeSurfer e.g the lh.aparc.annot into an ".nii" so i can see the parcels in Mricro. Now I can see the parcels just on the cortex not

[Freesurfer] Seeing Parcels as volumes

External Email - Use Caution Dear Douglas Greve; Thank you for your great help.I did what you said successfully.Now I have another question. I have used "mri_divide_parcellation" to have more parcels.this command gives me a ".annot" file.How can i change this file into a format

[Freesurfer] Saving the Results into the Original Space

External Email - Use Caution Dear FreeSurfer experts, How can I save the result of parcellation and segmentation into the original space? I would appreciate any help. Best regards, Maedeh___ Freesurfer mailing list Freesurfer@nmr.mgh.har

[Freesurfer] A Question about Estimating the Cortical Thickness for Each Subregion

External Email - Use Caution Dear Freesurfer Experts; I have a question, are there any ways in FreeSurfer to estimate the gray matter volume or cortical thickness of each region after parcellation, in order to define the edges in the brain network? Kind regards, Maedeh,__

[Freesurfer] A Question about Estimating the Cortical Thickness for Each Subregion

External Email - Use Caution Dear Dr.Bruce Fischl, Thanks for helping me, actually in other words, i am gonna make my brain network based on the graph theory, the nodes of my graph are the parcels and for the edges between the nodes i am gonna compute the cortical thickness or

[Freesurfer] Seeing the Results in the Original Space

External Email - Use Caution Dear FreeSurfer Experts, How can i have the results of FreeSurfer in its original space? The results have rotation and also the axial and the coronal images are replaced with each other. Thanks in advance Best regards, Maedeh___

[Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"

External Email - Use Caution Dear Freesurfer experts, I am using "mris_divide_parcellation" in order to increase the region numbers of Freesurfer parcellation output using "recon-all". e.g i have a 200-region parcellation.Now i wanna use "mris_ca_train" and this .annot file as

[Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"

External Email - Use Caution Dear Freesurfer experts, I am using "mris_divide_parcellation" in order to increase the region numbers of Freesurfer parcellation output using "recon-all". e.g i have a 200-region parcellation.Now i wanna use "mris_ca_train" and this .annot file as

[Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"

External Email - Use Caution Dear Dr.Bruce Fischl Thank you very much for your great sense of responsibility. Sure, i have sent you a zip file named "Maedeh_results"(it was a rather big sized one so i had to send it through Wetranser). Hope you have received it. However, a general

[Freesurfer] using mris_ca_train

External Email - Use Caution Dear Freesurfer experts, I have a question, does the number of input subjects matter in using "mris_ca_train" or not? i mean does it affect the results?(maybe the more subjects, the better result) and if yes, what is an approximate number? and the sec

[Freesurfer] Functional Connectivity in FreeSurfer

External Email - Use Caution Dear FreeSurfer experts, I have a general question, if i have a parcellation(an annotation file e.g aparc.annot which is the output of FreeSurfer) is FreeSurfer able to calculate the functional connectivity between the regions(parcels) using rs-fMRI

[Freesurfer] Installing Two Versions of FreeSurfer on One System at the Same Time

External Email - Use Caution Dear FreeSurfer experts, I wonder if I can install two versions of FreeSurfer (the latest one and an older one) on one system at the same time. Thanks more. Best Maedeh,___ Freesurfer mailing list Freesurfer@

[Freesurfer] Problem in Installing FreeSurfer on Mint19

External Email - Use Caution Dear experts, Thank u very much for all the help so far I have mint19 on my system and I have installed FreeSurfer on it. when I run a command like "mri_convert" it is ok. But when I run "recon-all" and some other commands, I see the error below : ba

Re: [Freesurfer] Problem in Installing FreeSurfer on Mint19

External Email - Use Caution Dear Tim, I did it successfully, Thanks more... Best Maedeh___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Registering Anatomical Parcellation to DWI

External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can Free

[Freesurfer] Necessity of Matlab for Using FsFast

External Email - Use Caution Dear experts, Is it necessary to install Matlab to use FsFast for functional connectivity? Thanks in advance Best Maedeh,___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.

[Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation

External Email - Use Caution Dear experts, I have a question, if I have a parcellation which is not the output of FreeSurfer, can i increase the number of its parcels in FreeSurfer? Maybe if I can change my file into an annotation file is it possible? I would be grateful if u

Re: [Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation

External Email - Use Caution Dear Bruce The parcellation I have is not on surface, it is volumetric. I wanna increase the number of its ROIs, I thought maybe I can change it into an annotation file and then use "mris_divide_parcellation". Hope it is clear enough now. Best Maedeh__

[Freesurfer] Excluding Specific Regions from a Volumetric File

External Email - Use Caution Dear FreeSurfer experts, I have used "mri_aparc2aseg" in order to map my parcellation file to a volumetric file, but in the end I wanna exclude some regions which I know their labels. I think it must be opposite of what "mri_binarize" does. I wonder h

[Freesurfer] Excluding Specific Regions from a Volumetric File

External Email - Use Caution Dear FreeSurfer experts, I have used "mri_aparc2aseg" in order to map my parcellation file to a volumetric file, but in the end I wanna exclude some regions which I know their labels. I think it must be opposite of what "mri_binarize" does. I wonder h

[Freesurfer] Visualizing Volumetric Files on Surface

External Email - Use Caution Dear FreeSurfer experts; I have created some volumetric(.nii) files in FreeSurfer (the procedure is as following: lh/rh.aparc.annot> mri_divide_parcellation > mri_aparc2aseg > deleting subcortical and white matter regions in order to keep just cortica

[Freesurfer] Fwd: Visualizing Volumetric Files on Surface

External Email - Use Caution > From: "Maedeh Khalilian" > To: "freesurfer@nmr.mgh.harvard.edu" > Date: Thu, 09 May 2019 01:24:58 +0430 > Subject: Visualizing Volumetric Files on Surface > Dear FreeSurfer experts; > I have created some vol

[Freesurfer] A Question Regarding Smoothing a Surface

External Email - Use Caution Dear experts, I have a parcellation scheme (an annotation file). Now I wanna smooth the map for better visualization. The command "mri_surf2surf" can do it ,but it doesn't recognize .annot. Now I wonder how to do it. I would appreciate it if u could

[Freesurfer] A Question Regarding the Command "mris_divide_pacellation"

External Email - Use Caution Dear experts, I use the file "lh/rh.aparc.annot" and a splitfile as the inputs of the command "mris_divide_parcellation" in order to have a parcellation with more regions. Now I have a question: for example if in my splitfile I write 4 in front of th

[Freesurfer] A Question Regarding the Command "mris_divide_pacellation"

aedeh I think it divides along the maximum variance eigen-axis, so should be repeatable. cheers Bruce On Thu, 6 Jun 2019, Maedeh Khalilian wrote: > > External Email - Use Caution > > Dear experts, > I use the file "lh/rh.aparc.annot" and a splitfile

[Freesurfer] A Question Regarding Topology Correction

External Email - Use Caution Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology correction through its routine pipeline using "recon-all" . However, I have some T2w brain MR images and I have done the segmentation and extracte

[Freesurfer] Fwd: A Question Regarding Topology Correction

External Email - Use Caution From: "Maedeh Khalilian" To: "freesurfer@nmr.mgh.harvard.edu" Date: Thu, 11 Jul 2019 07:37:05 +0430 Subject: A Question Regarding Topology Correction Dear FreeSurfer experts, I know that FreeSurfer does segmentation, su

[Freesurfer] A Question Regarding Topology Correction

External Email - Use Caution Dear Bruce, The other day I asked you about doing topology correction on my own segmentation(I have put my first e-mail and you response in the following so u can track easier). according to what you suggested, I have created a synthetic T1 volume b