Re: [Freesurfer] segmentHA on Human Connectome Project

2020-10-19 Thread AmirHussein Abdolalizadeh
External Email - Use Caution Thanks for your reply Eugenio. I renamed a few files in the /mri folder: aseg.mgz → aseg.1mm.mgz aseg.hires.mgz → aseg.mgz brain.mgz → brain.1mm.mgz brain.hires.mgz → brain.mgz filled.mgz → filled.1mm.mgz filled.hires.mgz → filled.mgz norm.mgz →

Re: [Freesurfer] Problem with dcmunpack on freesurfer

2020-10-19 Thread fsbuild
External Email - Use Caution Hello Praveen, The first line of dcmunpack script should indicate it calls the tcsh interpreter.  However, neither csh or tcsh interpreters are installed by default on Ubuntu.  The "which" command will probably report it is not found on your system t

[Freesurfer] Error during skullstripping: numerical result out of range

2020-10-19 Thread Hye Min Shin
External Email - Use Caution Hi experts, While running recon-all on subjects with 3T T1 scans, I ran into an error with one subject during skullstripping stage. Recon-all was running with 3T flag. The error message is the following: register_mri: find_optimal_transform find_opti

[Freesurfer] Problem with dcmunpack on freesurfer

2020-10-19 Thread Praveen Raghunathan
External Email - Use Caution Hi Freesurfer developers, Sorry if I'm making a simple mistake that I've overlooked. I am currently trying to do the freesurfer tutorials available at http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials and am having problems with the dcmunpack command

[Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects

2020-10-19 Thread 李梦君
External Email - Use Caution Dear FreeSurfer Developers: I compared the thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area, I defined the statistic difference regio

[Freesurfer] why can't I receive a reply from others in my mailbox?

2020-10-19 Thread 1248742467
External Email - Use Caution Hello,  After i asked a question, why can't I receive a reply from others in my mailbox?___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] replace the vertex_label_index in .annot file

2020-10-19 Thread 1248742467
External Email - Use Caution hello, Previously, rh.white and rh.aparc.2009s.annot were used to generate vertex_id and vertex_label,  ' from freesurfer_surface import Surface from freesurfer_surface import Label from freesurfer_surface import Annotation surface = Surface.read_tri

Re: [Freesurfer] Tracula error: run list is longer than subject list

2020-10-19 Thread Yendiki, Anastasia
Make sure to use "subjlist", not "sublist". If that is not the issue, then please attach your log file and configuration file - it's hard to guess the issue without more information. Best, Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Sha

Re: [Freesurfer] surf pial_lgi not created in version 7.1.0

2020-10-19 Thread Kathy L. Pearson
External Email - Use Caution I am getting this error near the tail of the 7.1.0 recon-all.log file just before exit: ERROR: find_corresponding_center_FSformat did not complete successfully! At this link from May 13: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] Exited with errors, segmentation fault

2020-10-19 Thread Hoopes, Andrew
Hi Julia, This is a small bug that's been fixed in the 7.1.1 patch release. I would recommend updating freesurfer versions (there will be no differences in recon-all results). Best, Andrew On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Julia Lam" wrote:

[Freesurfer] Tracula error: run list is longer than subject list

2020-10-19 Thread Shanika Jayakody
External Email - Use Caution Hello, I have been trying to run trac-all on a DWI of a participant, but I keep getting the error "run list is longer than subject list" I have created a configuration file setting sublist and runlist to just one subject so I am not sure what the err

[Freesurfer] fwhm values for gyrification index analysis

2020-10-19 Thread vittal korann
External Email - Use Caution Hi Doug I'm analyzing the gyrification values between schizophrenia and healthy volunteers. While performing group analysis in QDEC, I encountered an error when setting the smoothing (fwhm) parameter to 25. Here is the error message from the terminal o

Re: [Freesurfer] Problem of the Mapping Label to the Subject

2020-10-19 Thread 李梦君
External Email - Use Caution Thank you very much, I will try surface analysis with command in 7.1.1 version -原始邮件- 发件人:"Wang, Ruopeng" 发送时间:2020-10-20 00:39:56 (星期二) 收件人: "李梦君" 抄送: "Freesurfer support list" 主题: Re: [Freesurfer] Problem of the Mapping Label to the Subje

Re: [Freesurfer] Problem of the Mapping Label to the Subject

2020-10-19 Thread Wang, Ruopeng
Sorry I was commenting on the screenshots in your previous email. I thought they were from freeview. We do not support Qdec anymore in 7.x versions. Ruopeng On Oct 19, 2020, at 11:09 AM, 李梦君 mailto:meng...@csu.edu.cn>> wrote: External Email - Use Caution Thanks for your help, I have

Re: [Freesurfer] Creating ROI from sig.mgh

2020-10-19 Thread Douglas N. Greve
Try using the correction for multiple comparisons (mri_glmfit-sim). Set the CWP threshold to 1.0 to get all the clusters. It will create a table with GI values for each cluster. Run mri_glmfit-sim with --help and/or look on line to get more info On 10/14/2020 3:55 PM, Basavaraju, Rakshathi wr

Re: [Freesurfer] Problem of the Mapping Label to the Subject

2020-10-19 Thread Douglas N. Greve
There is no QDEC in 7.X, we have abandoned it. On 10/19/2020 11:09 AM, 李梦君 wrote: External Email - Use Caution Thanks for your help, I have tried FS 7.1.1, while there is no Qdec command when I tried FS 7.1.1 in the terminal window. How should I start the Qdec in the 7.1.1 version.

Re: [Freesurfer] Error sending tcl command

2020-10-19 Thread Douglas N. Greve
We are no longer support tksurfer. You can try using freeview. If you run tksurferfv, it will run freeview with most of the tksurfer command line options On 10/14/2020 11:42 PM, Kothapalli, Satya wrote: External Email - Use Caution Hi Expert, I am trying to render the surface maps u

Re: [Freesurfer] Help with creating contrast matrix - 6 classes and 3 variables

2020-10-19 Thread Douglas N. Greve
With 6 classes and 3 variables, you will have 24 regression coefficients and so 24 items in your contrast matrix (so good, so far). The order will be 1. MaleMaxT-Offset 2. MaleKahn-Offset 3. 4. 5. 6. 7. MaleMaxT-AgeSlope 8 9 10 11 12 13 MaleMaxT-HRSD_Reduction-Slope 14 MaleKahn-HRSD_Reduction-Slo

Re: [Freesurfer] Estimating the memory footprint of Longitudinal Stream?

2020-10-19 Thread Douglas N. Greve
I don't know. Each command will have an fs_time output which will have a measure of the peak memory used, though it is not super accurate. Alternatively, I could add something to mri_fuse_segmentations to periodically print out the peak memory usage On 10/13/2020 3:01 PM, Paul Wighton wrote:

Re: [Freesurfer] Problem of the Mapping Label to the Subject

2020-10-19 Thread 李梦君
External Email - Use Caution Thanks for your help, I have tried FS 7.1.1, while there is no Qdec command when I tried FS 7.1.1 in the terminal window. How should I start the Qdec in the 7.1.1 version. Best wishes Mengjun Li -原始邮件- 发件人:"Wang, Ruopeng" 发送时间:2020-10-19

Re: [Freesurfer] amygdala segmentation on anatomy

2020-10-19 Thread Douglas N. Greve
You have to run recon-all on your T1-weighted image (see the tutorials on the wiki), then run the hippo/amyg segmentation as found here https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala On 10/13/2020 12:32 PM, Elena Aggius-Vella wrote: External Email -

Re: [Freesurfer] Qdec - talairach to vertex for display purposes

2020-10-19 Thread Douglas N. Greve
We don't use qdec anymore, so I can't remember what the interface is like. You can transfer your coordinates to fsaverage space, see https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems and then go to that point in freeview On 10/13/2020 9:45 AM, Paul Dhami wrote: External Ema

Re: [Freesurfer] The usage about annotation view

2020-10-19 Thread Douglas N. Greve
I don't understand what you are saying. Can you elaborate? On 10/13/2020 8:31 AM, 1248742467 wrote: External Email - Use Caution hello, FreeSurfer I have loaded rh.pial and rh.aparc.2009s.annot, why my version does not have the label view option that can see the annotation? Is it a

Re: [Freesurfer] Put the updated vertex_label into .annotation

2020-10-19 Thread Douglas N. Greve
Use mris_label2annot Run with --help to get examples On 10/13/2020 8:22 AM, 1248742467 wrote: External Email - Use Caution hello, After I updated the vertex_label of rh.aparc.a2009s.annot with an algorithm, now I want to replace the vertex_label in the .annot with the updated vertex_

Re: [Freesurfer] asegstats2table error with options --etiv and --no-vol-extras

2020-10-19 Thread Douglas N. Greve
What happens if you don't include --segno ? On 10/13/2020 8:11 AM, Rovai Antonin wrote: > External Email - Use Caution > > Hello, > > when using asegstats2table with the two flags --etiv and --no-vol- > extras, I get the following error: > > ERROR: --etiv, cannot find EstimatedTotalIntraC

Re: [Freesurfer] Moving .nii atlas to surface space and create .annot file

2020-10-19 Thread Douglas N. Greve
On 10/13/2020 5:42 AM, Maron M. wrote: > External Email - Use Caution > > Dear Freesurfer Team, > > I need to move an atlas file, Shen268 in 2mm > (https://www.nitrc.org/frs/download.php/7977/shen_2mm_268_parcellation.nii.gz) > from volumetric into surface space in order to do some anal

Re: [Freesurfer] display results with tksurfer

2020-10-19 Thread Douglas N. Greve
Not sure, we don't use tksurfer that much anymore. Have you tried freeview? You can run freeview with tksurferfv and the same tksurfer arguments (makes it easier) On 10/13/2020 5:03 AM, Marina Fernández wrote: External Email - Use Caution Dear Freesurfer experts, I would like to mod

Re: [Freesurfer] mapping function of 3d coordinates of brain surface to latitude and longitude of a sphere

2020-10-19 Thread Douglas N. Greve
No sure what you are trying to do. Each  vertex on the surface has several  coordinates associated with it. Eg, a given vertex on the white surface will have a coordinate in the volume space (see https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems); that same vertex in the ?h.sphere.reg

Re: [Freesurfer] Display results

2020-10-19 Thread Douglas N. Greve
Load it as a volume using freeview On 10/11/2020 4:42 PM, Valentina Mancini wrote: External Email - Use Caution Thank you for this answer. How should I load aparc a2009+aseg.mgz for visualization and load a color map with p-values? If I  load the fsaverage with the command "tksurf

Re: [Freesurfer] Error with pial delineation

2020-10-19 Thread Douglas N. Greve
That is fine. The surface has to cross the ventricle at some point On 10/9/2020 2:09 PM, Julie Ottoy wrote: External Email - Use Caution Dear Freesurfer team, I have a question regarding the freesurfer delineation of the subject in attachment. Here the pial delineation crosses the ve

Re: [Freesurfer] surf pial_lgi not created in version 7.1.0

2020-10-19 Thread Douglas N. Greve
Can you send the recon-all.log file? On 10/9/2020 12:47 PM, Kathy L. Pearson wrote: > External Email - Use Caution > > No, it does not exist, and my question is why not in 7.1.0 when it is created > with the same two commands in 5.3.0? > > Thanks, > > Kathy > > >> Douglas N. Greve Fri, 0

Re: [Freesurfer] recon-all -s -autorecon2-cp -autorecon3 error

2020-10-19 Thread Douglas N. Greve
Those control points are still in gray matter. Please remember to post to the list, thanks On 10/9/2020 11:18 AM, Kazuki Sakakura wrote: External Email - Use Caution Thank you for continuously helping me. With your comment, I performed to put some control points in WM (attached image

Re: [Freesurfer] Seed region in anatomical data for resting state fMRI data

2020-10-19 Thread Douglas N. Greve
On 10/8/2020 8:31 PM, Gwang-Won Kim wrote: External Email - Use Caution Hi there, I obtained a seed region (left superior frontal)from anatomical data to process resting state fMRI data as follows: fcseed-sess -o lh.SFC.dat -segid 1028 -s session -fsd rest. I wonder if what the see

Re: [Freesurfer] Problem of the Mapping Label to the Subject

2020-10-19 Thread Wang, Ruopeng
I think this is a bug in freeview from FS 6.0.0 that has been fixed in 7.x. Would it be possible for you to try FS 7.1.1? A quick workaround you may try first is to change the offset for the inflated surface to 0 0 0 in freeview 6.0.0. Best, Ruopeng On Oct 19, 2020, at 2:38 AM, 李梦君 mailto:men