[Freesurfer] Question about how to build .gca files from non-human atlas and images

2019-09-04 Thread arsene ella
External Email - Use Caution *Dear **Freesurfer experts,* *I’ve built an atlas of structures of a non-human average brain and now **I would like to build **its** .gca files from scratch. **From the Freesurfer mailing list, I saw that this is possible using **rebuild_gca_atlas.csh*

[Freesurfer] Scale Option for mris_convert

2019-09-04 Thread roc...@netzero.net
External Email - Use Caution Hello, I normally use mris_convert --combinesurfs for generating STL files from the lh.pial and rh.pial. When running Freesurfer on my local computer, there are no problems with this approach and everything is perfect. However, the lh.pial and

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-04 Thread Rovai Antonin
External Email - Use Caution Hello I think there is a problem with the dicom files. I could not see it on the images before mri_convert -conform but there’s definitely something weird in there. I suspect it comes from some software that misexported the data. Running reconall on

Re: [Freesurfer] PALM Analysis

2019-09-04 Thread Greve, Douglas N.,Ph.D.
mri_glmfit-sim will do it, GRF or permutation On 9/4/19 1:33 PM, Harikumar, Amritha wrote: > Hello, > > Thanks for letting me know regarding running fsPalm in your previous message. > My next question is - what command can we use in Freesurfer that can run > multiple comparison testing for

Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels

2019-09-04 Thread Diers, Kersten /DZNE
External Email - Use Caution Hi, I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file? If my

[Freesurfer] PALM Analysis

2019-09-04 Thread Harikumar, Amritha
Hello, Thanks for letting me know regarding running fsPalm in your previous message. My next question is - what command can we use in Freesurfer that can run multiple comparison testing for subcortical regions? If not fsPalm, is there another function that will perform this? Thanks, Amritha

Re: [Freesurfer] FreeView : Tools : Volume Filter : Close

2019-09-04 Thread Bruce Fischl
Hi Yar, close is a morphological close operation, which in the grayscale case is a max followed by a min I believe (in a 3x3x3 nbhd) cheers Bruce On Wed, 4 Sep 2019, Yasir Hadi wrote: External Email - Use Caution Hello FreeSurfer Developers, I just want to get the

Re: [Freesurfer] recon_all cuda 9.1

2019-09-04 Thread Dev vasu
External Email - Use Caution Dear, I tried running recon-all -s subjectname -t subjectid -all -openmp 15 , and it still runs very slowly. Is there a faster way to reduce the recon-all time using openmp, please kindly suggest me. Thanks Vasudev On Sat, Aug 31, 2019 at 11:43 AM

Re: [Freesurfer] paired t-test for pet surface analysis

2019-09-04 Thread Greve, Douglas N.,Ph.D.
If you are going to do a paired test, then each subject can only have 2 time points On 9/4/19 11:58 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Hello Freesurfer, > > I am trying to run a surface based paired ttest for pet. I started by > running mri_vol2surf for each

[Freesurfer] paired t-test for pet surface analysis

2019-09-04 Thread miracle ozzoude
External Email - Use Caution Hello Freesurfer, I am trying to run a surface based paired ttest for pet. I started by running mri_vol2surf for each pet longitudinal subject. However, when i use mri_concat with --f, --prune, and --paired-diff i get an error " --paired-xxx specified

Re: [Freesurfer] PETsurf kinetic modeling with MRTM

2019-09-04 Thread Chanmi Kim
External Email - Use Caution Hi Douglas, I checked dicom headers by using ‘dicom_hinfo’ command to get the information of the acquisition time that each frame was acquired. dicom_hinfo -tag 0008,0032 *.dcm Here is the information of the acquisition times: 16:40:08

Re: [Freesurfer] make_average_subject error

2019-09-04 Thread Greve, Douglas N.,Ph.D.
Is BrainaverageN72 in the subjects list? On 9/3/19 12:39 PM, Maxime Perron wrote: > > External Email - Use Caution > > ​Dear Freesurfer Experts, > > > I have the following issue when running the make_average_subject command ( > > make_average_subject --subjects (Subjid) --out

Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

2019-09-04 Thread Greve, Douglas N.,Ph.D.
On 9/3/19 12:05 PM, cody samth wrote: > > External Email - Use Caution > > Hello, > > I have a question regarding how to graph results that came from a > vertex wise analysis using the command mri_glmfit and mri_glmfit-sim. > > I was interested in investigating an interaction effect

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-04 Thread Bruce Fischl
glad to hear it worked out (and it wasn't our fault!) cheers Bruce On Wed, 4 Sep 2019, Rovai Antonin wrote: External Email - Use Caution Hello I think there is a problem with the dicom files. I could not see it on the images before mri_convert -conform but there’s definitely

[Freesurfer] FreeView : Tools : Volume Filter : Close

2019-09-04 Thread Yasir Hadi
External Email - Use Caution Hello FreeSurfer Developers, I just want to get the Information: which parameters are used as I apply the filter *Close* on the volume dataset using the FreeView Version 2.0 Builed Jan 18 2017 16:48:55. I've searched the list and the wiki and I

Re: [Freesurfer] FreeView : Tools : Volume Filter : Close

2019-09-04 Thread Ruopeng Wang
Hi Ysr, I think it just uses a 3x3x3 kernel. Best, Ruopeng On 9/4/19 10:51 AM, Yasir Hadi wrote: External Email - Use Caution Hello FreeSurfer Developers, I just want to get the Information: which parameters are used as I apply the filter *Close* on the volume dataset using the

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"

2019-09-04 Thread Caspar M. Schwiedrzik
External Email - Use Caution Hi! I am following up on this thread trying to understand how to make the color wheel visible in rtview, or, if necessary, in freeview. Thank you! Caspar ___ Freesurfer mailing list

Re: [Freesurfer] Compare vertexwise correlation maps

2019-09-04 Thread Greve, Douglas N.,Ph.D.
I'm not sure you can. Unless you have multiple samples, you can't compute a variance. If you can't compute a vvariance, then  you can't compute a significance. Maybe you can do some kind of bootstrapping On 9/3/19 1:49 PM, Matthieu Vanhoutte wrote: > External Email - Use Caution > > So

Re: [Freesurfer] Clusterwise correction for multiple comparisons

2019-09-04 Thread Greve, Douglas N.,Ph.D.
If it is only one space, then you can just leave off --3spaces On 9/3/19 1:48 PM, Gwang-Won Kim wrote: > > External Email - Use Caution > > Hi there, > To perform a cluster-wise correction for multiple comparisons, I ran > monte carlo simulation as follows: mri_glmfit-sim --glmdir

Re: [Freesurfer] make_average_subject error

2019-09-04 Thread Maxime Perron
External Email - Use Caution Hi Greve, The exact script is the following : setenv SUBJECTS_DIR /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003"

Re: [Freesurfer] recon_all cuda 9.1

2019-09-04 Thread Bruce Fischl
Hi Vasudev what does "very slowly" mean? cheers Bruce On Wed, 4 Sep 2019, Dev vasu wrote: External Email - Use Caution Dear, I tried running recon-all -s subjectname -t subjectid -all -openmp 15 , and it still runs very slowly. Is there a faster way to reduce the recon-all

Re: [Freesurfer] Question about how to build .gca files from non-human atlas and images

2019-09-04 Thread Greve, Douglas N.,Ph.D.
Sorry, I think this is beyond our ability to support. On 9/4/19 4:44 AM, arsene ella wrote: > > External Email - Use Caution > > /Dear //Freesurfer experts,/ > > /I’ve built an atlas of structures of a non-human average brain and now //I > would like to build //its//.gca files from

Re: [Freesurfer] make_average_subject error

2019-09-04 Thread Greve, Douglas N.,Ph.D.
Can you send the full text of the terminal output? On 9/4/19 10:44 AM, Maxime Perron wrote: > External Email - Use Caution > > Hi Greve, > > The exact script is the following : > > > setenv SUBJECTS_DIR >

Re: [Freesurfer] Scale Option for mris_convert

2019-09-04 Thread Greve, Douglas N.,Ph.D.
That scales the coordinates and will have no effect on the file size. Try mris_decimate instead. Note that the version 6 mris_decimate is not deterministic. I've put a deterministic one here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_decimate On 9/4/19 2:49 PM, roc...@netzero.net

Re: [Freesurfer] Siemens Enhanced DICOM

2019-09-04 Thread Greve, Douglas N.,Ph.D.
Try using dcm2niix (not part of FreeSurfer) to convert to nifti On 9/4/19 3:44 PM, Funk, Quentin wrote: > > External Email - Use Caution > > Hey all- > > Freesurfer's recon-all fails if I try to give it a dicom from the new > Siemens Enhanced format. Are there any workarounds that don't

[Freesurfer] Invaild Key Error for Freesurfer 5.1

2019-09-04 Thread An Lijun
External Email - Use Caution Dear Freesurfer experts, Right now I am trying to use Freesurfer 5.1.0. But the software showed ERROR “Invalid FreeSurfer license key found in license file”. We tried to apply license online, however, the license provided online is now for 6.0.0

Re: [Freesurfer] make_average_subject error

2019-09-04 Thread Maxime Perron
External Email - Use Caution Good evening Greve, Thanks for your quick answer. I attached the file containing the output. Best, Maxime recon-all.log Description: recon-all.log > On Sep 4, 2019, at 6:10 PM, Greve, Douglas N.,Ph.D. > wrote: > > Can you send the full text

Re: [Freesurfer] Invaild Key Error for Freesurfer 5.1

2019-09-04 Thread fsbuild
External Email - Use Caution Hello An, My understanding is that in Freesurfer 5 you need to have a file called “.license” and it should be placed in the directory where you installed freesurfer. That directory is also the path the variable $FREESURFER_HOME points to. So if

[Freesurfer] Siemens Enhanced DICOM

2019-09-04 Thread Funk, Quentin
External Email - Use Caution Hey all- Freesurfer's recon-all fails if I try to give it a dicom from the new Siemens Enhanced format. Are there any workarounds that don't involve converting to nifti with a different software first? Thanks! Quentin Funk, PhD Houston Methodist

Re: [Freesurfer] Invaild Key Error for Freesurfer 5.1

2019-09-04 Thread fsbuild
External Email - Use Caution Hello An, Try taking the attached file “license_5” and rename it to “.license” Then put it under $FREESURFER_HOME so that you see it when you issue the command, $ ls $FREESURFER_HOME/.license - R. On Sep 4, 2019, at 22:50, fsbuild