Re: [Freesurfer] ERROR: nu_correct

External Email - Use Caution Dear Sevan, Which version of FreeSurfer are you running on which system (Mac, Linux?), and what is the exact command line and error message? In case it is about nu_correct not being found: it should be in $FREESURFER_HOME/mni/bin/nu_correct, and if

[Freesurfer] Convert Yeo's 17-network confidence map into MNI152 volumetric space

External Email - Use Caution Dear FreeSurfer experts and users, I would like to convert Yeo's 17-network confidence map into MNI152 volumetric space and I tried the following commands (but failed): (1) mri_surf2vol --so $SUBJECTS_DIR/fsaverage/surf/lh.white $SUBJECTS_DIR/fsave

[Freesurfer] Custom Colormap

External Email - Use Caution Hello! I would like to ask you about customs colormaps. I have created my own FreeSurferColorLUT.txt and I would like configure the color map using command line. Is it possible? Thanks in advance. Emanuel __

Re: [Freesurfer] Custom Colormap

Hi Emanuel can you tell us more. For parellations or segmentations? Are you just changing the color of existing parcels/segments? If so you can just import it in freeview cheers Bruce On Mon, 1 Apr 2019, Emanuel Alvaredo wrote: External Email - Use Caution Hello! I would l

Re: [Freesurfer] Custom Colormap

External Email - Use Caution Thanks for the answer Bruce. Is For segmentations. I have run freesurfer for 100 nomal patients. I have calculated standard desviation and mean, then I am comparing the results against a patological patient. So, I would like to open freeview, for examp

Re: [Freesurfer] Custom Colormap

I see. You can give freeview a custom lookup table on the command line cheers Bruce On Mon, 1 Apr 2019, Emanuel Alvaredo wrote: External Email - Use Caution Thanks for the answer Bruce. Is For segmentations. I have run freesurfer for 100 nomal patients. I have calculated st

Re: [Freesurfer] Custom Colormap

External Email - Use Caution Thanks Bruce, Do you know what is the command line option? Thanks! Emanuel On Mon, Apr 1, 2019 at 11:34 AM Bruce Fischl wrote: > I see. You can give freeview a custom lookup table on the command line > > cheers > Bruce > > > On Mon, 1 Apr 2019, Eman

Re: [Freesurfer] Custom Colormap

Hi Emanuel, You can use this command to load customized color table file: freeview -v brain.mgz:colormap=lut:lut=color_table_file.txt Best, Ruopeng On 4/1/19 10:40 AM, Emanuel Alvaredo wrote: Thanks Bruce, Do you know what is the command line option? Thanks! Emanuel On Mon, Apr 1, 2019 at 1

Re: [Freesurfer] Custom Colormap

External Email - Use Caution Thanks! Emanuel On Mon, Apr 1, 2019 at 12:13 PM Ruopeng Wang wrote: > Hi Emanuel, > > You can use this command to load customized color table file: > > freeview -v brain.mgz:colormap=lut:lut=color_table_file.txt > > Best, > Ruopeng > On 4/1/19 10:40

Re: [Freesurfer] trouble converting between .mgz and .nii.gz

Not sure what is going on here. What is lh.atlas.mgz? Is is a surface overlay? What is subject_t1.nii.gz? If it is not the same geometry of lh.atlas.mgz, then strange things will happen when you do it a second time. On 3/31/2019 12:28 PM, JD Knotts wrote: External Email - Use Caution H

[Freesurfer] segmentHA_T1.sh

External Email - Use Caution Hello, I have finished running segmentHA_T1.sh on my data and have gotten all the .mgz and .txt files in my mri folder. I would like to collect all the hippocampal volumes and get them into a table to run stats on. When reading the documentation it sa

Re: [Freesurfer] trouble converting between .mgz and .nii.gz

External Email - Use Caution Hi Dr. Greve, Thanks very much for your reply! The lh.atlas.mgz file is a volumetric atlas (Kastner atlas ) generated for an individual subject as described here

[Freesurfer] segmentHA_T1.sh

External Email - Use Caution I thought a solution like this might work but there seems to be an issue reading in the file. I tried using mri_segstats on the .mgz file like this to create the stats file as this is what I do for my dt_recon results however it doesn't seem to work wh

Re: [Freesurfer] segmentHA_T1.sh

External Email - Use Caution How about quantifyHAsubregions.sh? Cheers, /E -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Daniel Callow Reply-To: Freesurfer support list Date: Monday, 1 April

Re: [Freesurfer] trouble converting between .mgz and .nii.gz

mri_info will give you the voxel-to-RAS matrix and the number of cols, rows, slices. I don't think those commands are doing what you think. I don't understand where vol2surf or cor2label come in. On 4/1/19 12:55 PM, JD Knotts wrote: > > External Email - Use Caution > > Hi Dr. Greve, > >

Re: [Freesurfer] segmentHA_T1.sh

External Email - Use Caution Thank you for the suggestion. Is it possible to just calculate certain sub-field volumes such as the head body and tail as opposed to all of them? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab Uni

[Freesurfer] Changing colour of clusters generated after MonteCarlo Correction

External Email - Use Caution Dear experts, Is it possible to change the colour of the clusters generated after using Monte Carlo Corrections? I would like to have it either blue or red to represent thinning or thickening respectively, since there are many different cluster col

Re: [Freesurfer] Changing colour of clusters generated after MonteCarlo Correction

In addition to the annotation, there is a surface segmentation ("seg") that is also produced by mri_glmfit-sim. You can convert the seg to an annotation by using mris_seg2annot, which will take a color table that you supply. Run it with --help to get more info. On 4/1/2019 1:24 PM, Arsenije Sub

[Freesurfer] implausible values of BrainSegVolNotVent

External Email - Use Caution Dear experts, I noticed suspicious values of segmentation volume in aseg.stats in subjects processed with version 6, with recon-all modified for HCP data. There is striking difference between BrainSegVolNotVent and BrainSegVolNotVentSurf. The v

Re: [Freesurfer] implausible values of BrainSegVolNotVent

Hi Antonin, I think this is a bug. Can you send me the recon-all.log file? thanks doug On 4/1/19 5:49 PM, Antonin Skoch wrote: > > External Email - Use Caution > > Dear experts, > > I noticed suspicious values of segmentation volume in aseg.stats in > subjects processed with version 6, wi