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

Re: [Freesurfer] create ctab from annot

You can use mri_annotation2label to extract a color table from the annotation On 12/03/2018 07:06 PM, Bruce Fischl wrote: > Hi Stephanie > > can you give us some details about how you generated your fine-grained > parcellation? > > cheers > Bruce > On Mon, 3 Dec 2018, Winkelbeiner, Stephanie A w

Re: [Freesurfer] create ctab from annot

Hi Stephanie can you give us some details about how you generated your fine-grained parcellation? cheers Bruce On Mon, 3 Dec 2018, Winkelbeiner, Stephanie A wrote: External Email - Use Caution Hi freesurfer-experts,   I used a customized script that produces a more fine-g

[Freesurfer] create ctab from annot

External Email - Use Caution Hi freesurfer-experts, I used a customized script that produces a more fine-grained parcellation resulting in an .annot file. I don't seem to have a look-up-table (LUT), however. I tried the following: - mri_annotation2label --> allows me t

[Freesurfer] fMRI time series extraction

External Email - Use Caution Hello FreeSurfer Experts, Now I have a custom annotation file (only the cortical surface). May I ask how could I use it to extract the mean time series from the fsfast-preprocessed fMRI data? I have tried to transform this annotation file into anatomic

[Freesurfer] Set annotation cluster color

External Email - Use Caution Dear Freesurfer Expert, Can I change the color of loading from the annot file in Freeview? Thanks a lot! Best regards, Ting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

Re: [Freesurfer] When no control points are needed...

External Email - Use Caution Hi Diamond! I think I did it. Thank you very much!! freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/loca

Re: [Freesurfer] When no control points are needed...

Hi Rosalia, Within the FTP interface, you need to write "put two_different_problems.txt". It seems like you only wrote the file name. Also, the example we provide is "filename.txt", make sure you write your file name - only include ".txt" if your file has that extension. Let me know if you h

Re: [Freesurfer] FTP issues [was: When no control points are needed...]

External Email - Use Caution That looks fine. You are logged in and you changed the directory. Just put the file now: put (In general the command depends on your FTP client, but a 'put' command should be available in every FTP client I guess.) A general note: you may be

[Freesurfer] mris_preproc paired diff outputs 0 values

External Email - Use Caution Hello, I am trying to do a paired difference analysis of two runs of probtrackx (I have already put them on the surface). The two conditions are “central” and “far” for each subject. I have already checked the individual subjects data and it does ind

[Freesurfer] Warping fsaverage maps to MNI152 volume

External Email - Use Caution Hello, I have a significance map I obtained through some analysis I did in Matlab. It's currently in fsaverage space. I want to move it to MNI152 space to compare with other results. From exploring the archives, it seems there are two ways of doing thi

Re: [Freesurfer] Surface displacement

External Email - Use Caution Dear Bruce, We resample the surface of the high resolution image to the low resolution image surface, then compare the surface of the original image to the resampled surface to calculate his surface displacement. What should we do? ---

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

I'm not sure why there is no error with the mri_convert function, but it somehow took in your BE2_T1.nii and creating a corrupted 001.mgz. The rawavg.mgz is just a copy of the 001.mgz, so it's no surprise that it has the same issues. You only get an error when recon-all attempts to run mri_conve

Re: [Freesurfer] When no control points are needed...

External Email - Use Caution Hi Bruce, This is the directory where I have the data: /home/rosalia/Desktop/transfer And I changed the directory before doing FTP...and then asked again for the directory and I wrote the same directory and then when asked me for the name of the fil

Re: [Freesurfer] Surface displacement

Hi yujunjie you need to give us more information than this. cheers Bruce On Mon, 3 Dec 2018, 1013364183 wrote: External Email - Use Caution Dear FS,  We want to calculate the displacement of different surfaces, what should we do? yours yujunjie ___

Re: [Freesurfer] When no control points are needed...

is that the right directory/path on your end? On Mon, 3 Dec 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Hi Bruce, Thank you for your reply. I am having problems when trying to upload the two files with FTP, it seems the problem is with the directory. ro

Re: [Freesurfer] When no control points are needed...

External Email - Use Caution Hi Bruce, Sorry for double posting. I am advancing, but there is still some point I am missing. I would greatly appreciate your help: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ cd /home/rosalia/Desktop/transferrosalia@rosalia-Lenovo-Y520-15IKBN ~/

[Freesurfer] Surface displacement

External Email - Use Caution Dear FS, We want to calculate the displacement of different surfaces, what should we do? yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/lis

Re: [Freesurfer] When no control points are needed...

External Email - Use Caution Hi Bruce, Thank you for your reply. I am having problems when trying to upload the two files with FTP, it seems the problem is with the directory. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh

Re: [Freesurfer] When no control points are needed...

Hi Rosalia you always have to run autorecon3 every time autorecon2 is run cheers Bruce On Mon, 3 Dec 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Dear Bruce and Bram, After improving the pial surface for my participants, I have seen that some of them

[Freesurfer] volume and mean intensity values from single nii file with multiple ROIs

External Email - Use Caution Dear All, I have segmented the midbrain of each subjects into different subregions (peduncle, substantia nigra, red nucleus etc) using an atlas. I am trying to extract the volume of each region (the regions are labeled 101, 102, 103 etc) and also tryin

Re: [Freesurfer] Problem in Installing FreeSurfer on Mint19

External Email - Use Caution Sounds like you do not have the tcsh shell installed on your system. There is no need to change your default shell from bash to tcsh, but you need tcsh installed for FreeSurfer to work. Have your system admin install it. Since Mint is Debian-based, t

[Freesurfer] When no control points are needed...

External Email - Use Caution Dear Bruce and Bram, After improving the pial surface for my participants, I have seen that some of them do not need control points. My question is: for those ones, should I run -autorecon2 and -autorecon3 or only -autorecon3. Hi Bruce and Bram, I wil

[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