Re: [Freesurfer] Freesurfer Digest, Vol 158, Issue 53

help Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von freesurfer-requ...@nmr.mgh.harvard.edu Gesendet: Donnerstag, 27. April 2017 19:24:57 An: freesurfer@nmr.mgh.harvard.edu Betreff: Freesurfer Digest, Vol 158, Issue 53 Send Freesurfer mailing list s

Re: [Freesurfer] Qdec 1.5

Hello Douglas Thank you for your response. I have just run the subjects from the data on OASIS through qdec and I followed the steps on freesurfer. Everything is ok until the step of pressing 'Generate Stats Data Tables' that I have asked you before somehow I keep getting the same issue. There is

[Freesurfer] mri_mcsim update and FreeSurfer6

I just read this statement : “ A newer version of mri_mcsim for linux can be obtained from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_mcsim.linux Copy it to $FREESURFER_HOME/bin/m

[Freesurfer] How to get SUVR images with cerebellar GM reference?

Hello PetSurfer and Freesurfer Developers, I am using PetSurfer to obtain PVC SUVR images . I have already used mri_concat to derive the mean images over three acquisitions (template image). After gtmseg amd mri_coreg, I want to get the SUVR map with whole cerebellum as the reference (instead o

[Freesurfer] Skull stripping

Dear FS experts, I want to inquire if there are any threshold for the flag "gcut " in the command: recon-all -skullstrip -clean-bm -gcut -subjid If this not available are there any tools that can help to control how much dura will be cut out Thanks in advance! John

Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table

Hi If I use my colorLookup table in annot file, then will mri_aparc2aseg will update that in FreeSurfurColorLUT.txt table. I am just trying to understand how mri_aparc2aseg works seeing the below text the extracted from FreeSurferColorLUT.txt. Still the voxel in apar+aseg.mgh does not showing

Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table

Hi Can you please explain what the flags mean here, I don't find them in help. mri_aparc2aseg --s 100307 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt

[Freesurfer] debug mri_aparc2aseg

Hi I need to debug the issue I am facing at the moment. So I want to run the program with GDB. I could run it with gdb but no debug information/symbol is present in the current installed form. So I guess I need to recompile the mri_aparc2aseg program with in debug mode. Can you please help me i

[Freesurfer] Implement my own parcellation on aparc+aseg.mgz file

Hi I have create my own annot file and lookuptable for cortical parcellation. How I can implement my own parcellation in aparc+aseg.mgz file. I am also stuck on how to update the FreeSurferColorLUT.txt file? Please help. Thanks Sarbani ___ Freesurfer m

Re: [Freesurfer] Implement my own parcellation on aparc+aseg.mgz file

Hi Das can you check if there is an embedded colormap in your .annot file?You can do this by running mris_info on it. cheers Bruce On Fri, 28 Apr 2017, Das S. wrote: > Hi > I have create my own annot file and lookuptable for cortical parcellation. > How I can implement my own parcellation in ap

Re: [Freesurfer] debug mri_aparc2aseg

Hi Sarbani if you have the source and build environment setup you can do a global replace of "-O3" with "-O0" in the Makefile in both utils and mri_aparc2aseg directories, then rebuild both cheers Bruce On Fri, 28 Apr 2017, Das S. wrote: > Hi > > I need to debug the issue I am facing at the

[Freesurfer] Long-stream comparing differing resolutions

Dear FS Experts, I’m trying to compare multiple T1-weighted sequences taken across multiple scanners in the same day in 15 individuals using the longitudinal stream. One question we had was how different cortical thickness estimates would be using a 0.8mm^3 resolution vs. our standard 1mm^3 MPRA

Re: [Freesurfer] Implement my own parcellation on aparc+aseg.mgz file

Yes there is embedded color file in my annot file. Here is the extract of lh.aparc.annot that I created. koushik@koushik-DQ77MK:~/Parcellation/100307_old/100307/label$ mris_info lh.aparc.annot reading colortable from annotation file... colortable with 95 entries read (originally 100307/label/eq

Re: [Freesurfer] Implement my own parcellation on aparc+aseg.mgz file

ok, then what is the next step in your processing? And where does it go wrong? Does the annot display in the proper colors on the surface? Sorry, I lost track of what was going on in your previous emails Bruce On Fri, 28 Apr 2017, Das S. wrote: > Yes there is embedded color file in my annot fil

Re: [Freesurfer] Implement my own parcellation on aparc+aseg.mgz file

Thank you for your reply and giving your time. I am not be able to figure out where things are going wrong. Then I followed the steps below of recon-all to create the apar+aseg.mgz file: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 10030

Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc

Here’s the script that I’m running and the merged stderr stdout. I’ve also tried various permutations of mris_sample_parc using the -t flag and using different LUTs than the one I made. Also copying the log here incase the text files get removed. Thanks, jared ./targetAnnotStats.sh: line 21

[Freesurfer] Using multiple MEMPRAGE scans as input to recon-all: which echos to use for dura correction?

Hi Freesurfer Experts! I have two scans for each subject in a new experiment—taken on subsequent days, each using the MEMPRAGE protocol. I’ve successfully implemented DURA correction using the 4 echos when I’ve reconstructed each scan separately. However, since I have 2 scans for each subject

Re: [Freesurfer] TRACULA anterior/posterior

Anastasia- This is super helpful! Thank you! I wrote a script to do exactly this and got something close (or exactly) to what I'm looking for, I think. However, there are very few voxels in the voxelwise file--I traced them out and they're essentially the hottest voxels stored in path.pd.ni

Re: [Freesurfer] Qdec 1.5

if that file does not exist, then it will crash. That file should be created by recon-all. Is that file not there? On 04/28/2017 05:22 AM, Duy Nguyen wrote: > Hello Douglas > > Thank you for your response. > I have just run the subjects from the data on OASIS through qdec and I > followed the s

Re: [Freesurfer] mri_mcsim update and FreeSurfer6

You do not need to update it, you can use the v6 version On 04/28/2017 05:24 AM, Damien MARIE wrote: > I just read this statement : “ A newer version of mri_mcsim for linux > can be obtained from here: > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_mcsim.linuxCopy > >

Re: [Freesurfer] How to get SUVR images with cerebellar GM reference?

add --rescale 7 8 46 47 these are the ids for left and right cblum wm and gm On 04/28/2017 06:13 AM, Shane Schofield wrote: > Hello PetSurfer and Freesurfer Developers, > > I am using PetSurfer to obtain PVC SUVR images . I have already used > mri_concat to derive the mean images over three acq

Re: [Freesurfer] Freesurfer Digest, Vol 158, Issue 53

Can you be more specific? On 04/28/2017 03:47 AM, Xenia Kobeleva wrote: > > help > > > *Von:* freesurfer-boun...@nmr.mgh.harvard.edu > im Auftrag von > freesurfer-requ...@nmr.mgh.harvard.edu > > *Gesendet:* Donnerstag,

Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table

You will need to create your own LUT, the FreeSurferColorLUT.txt will not be updated. Can you figure out how to do that from the extracted text below? On 04/28/2017 07:16 AM, Das S. wrote: > Hi > If I use my colorLookup table in annot file, then will mri_aparc2aseg will > update that in FreeSu

Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table

Answers below On 04/28/2017 07:34 AM, Das S. wrote: > Hi > Can you please explain what the flags mean here, I don't find them in help. > > mri_aparc2aseg --s 100307 --volmask --aseg aseg.presurf.hypos --relabel > mri/norm.mgz mri/transforms/talairach.m3z > /usr/local/freesurfer/average/RB_all

Re: [Freesurfer] Maps showing correlations between structural measures

To use the PVR, you need to create a stack of the measures that you want to use (eg, lGI). This will be the same size as the stack you want to correlate with. Eg, if you use mris_preproc to create a thickness stack, you would use the same command to create the lGI stack. Create your FSGD file a

Re: [Freesurfer] Using multiple MEMPRAGE scans as input to recon-all: which echos to use for dura correction?

Hi Jared it's really an empirical question. With high quality data we have found that adding scans doesn't help CNR very much (it reduced the N but the blurring induced by differential distortion also reduces the C). If your scans are noisy it might be worth it, but it really depends on the a

Re: [Freesurfer] TRACULA anterior/posterior {Disarmed}

Hi Quentin - Can you send me the table that you get from trac-all -stat? Thanks! a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Funk, Quentin [qf...@houstonmethodist.org] Sent: Friday, April 28, 2017 5:44 P

[Freesurfer] [FreeSurfer] cortical parcellation

Does freesurfer output individual roi volume masks for each of the cortical parcellations in aparc+aseg? thanks Joseph Veliz VA Hospital West LA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] [FreeSurfer] cortical parcellation

Hi Joseph you can use mri_binarize or mri_extract_labels to copy them out of the aparc+aseg into individual volume masks if you want cheers Bruce On Fri, 28 Apr 2017, VA Research wrote: Does freesurfer output individual roi volume masks for each of the  cortical parcellations in aparc+aseg?

Re: [Freesurfer] [FreeSurfer] cortical parcellation

No, you can do it with mri_binarize --i aparc+aseg.mgz --match ID --o roi.ID.nii.gz where ID is the parc id from the FreeSurferColorLUT.txt On 04/28/2017 06:58 PM, VA Research wrote: > Does freesurfer output individual roi volume masks for each of the > cortical parcellations in aparc+aseg? >

Re: [Freesurfer] TRACULA tract reconstruction

Hi Joelle - The last command in the trac-all.log file (mri_probedicom) works fine for me, when I run it on your dicoms. So there must be something else after that command that causes the error. What do you see when you run "ls /Users/joelle/Documents/Tracula_new/tmp/5047_3_3T.long.5047_3T_base/d