Re: [Freesurfer] (no subject)

Does it run with the --cpu flag? That will run it with the cpu and thus isolate your problem to the gpu/cuda On 9/9/2024 10:31 PM, Matthew Lynch wrote: External Email - Use Caution I run this command: mri_synthseg --i /mnt/p/test/test-t2-3mm.nii --parc --robust --o /mnt/p/test an

[Freesurfer] (no subject)

External Email - Use Caution I run this command: mri_synthseg --i /mnt/p/test/test-t2-3mm.nii --parc --robust --o /mnt/p/test and it fails with the following (partial) error message: Node: 'model_3/unet_conv_downarm_0_0/Conv3D' DNN library is not found. which I assume means it

Re: [Freesurfer] (no subject)

: Wednesday, July 17, 2024 8:18 AM To: Freesurfer support list Subject: Re: [Freesurfer] (no subject) External Email - Use Caution ​Thank you very much! Can the transform matrix be extracted out and imported to the 3d slicer. Thus I can realize the registration in the slicer -原始邮件- 发件

Re: [Freesurfer] (no subject)

pport list" 抄送: 主题: Re: [Freesurfer] (no subject) Freesurfer lh.pial and rh.pial xyz coordinates are reported in tkregister space. I believe you need to convert tkrRAS to RAS space using vox2ras * inv(vox2ras-tkr). ‘vox2ras’ and ‘vox2ras-tkr’ matrix are reported in mris_info. If you

Re: [Freesurfer] (no subject)

??? Sent: Monday, July 15, 2024 5:05 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] (no subject) External Email - Use Caution Dear Freesurfer Team I have extracted the left and right cerebral cortex from the aseg.mgz file in the 3d slicer. At the same time, I have

[Freesurfer] (no subject)

External Email - Use Caution Dear Freesurfer Team I have extracted the left and right cerebral cortex from the aseg.mgz file in the 3d slicer. At the same time, I have loaded the lh.pial and rh.pial in the 3d slicer the left and right cerebral cortex extracted from

[Freesurfer] (no subject)

External Email - Use Caution Hi. I need to be removed from the mailing list. Kindly help do the same. The id is sridevisundara...@gmail.com Regards Sridhevi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh

[Freesurfer] (no subject)

External Email - Use Caution Hi all, I am trying to convert freesurfer reconall output back in original subject space so I am following this guide: https://secure-web.cisco.com/1hdoEYpcNfh6v9Yoq-8Iexo7oO3DXo3uI45KMmpjSSOcduyIGyNK6kNk9t-Uwfp2Z0juQB6SnTwW1xT5nV4DA0YNU7AqiAvMOTcHLy4It

Re: [Freesurfer] (no subject)

External Email - Use Caution SVM is a segmentation/classification algorithm and does not give the inference that the GLM gives. Not sure what other models you are talking about On 8/21/2023 9:28 AM, 林 耀云 wrote: External Email - Use Caution Hi Freesurfer Team, I have

[Freesurfer] (no subject)

External Email - Use Caution Hi Freesurfer Team, I have a question can’t understand. Why just uses general linear model to analysis in Freesurfer? There are a lot of models such as nonlinear model, SVM and others. Please help me answer. Thank you so much. Additionally, as attac

Re: [Freesurfer] (no subject)

they were scanned. Best, Jackson From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Atwater, Emanuel R Sent: Thursday, July 27, 2023 6:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] (no subject) External Email - Use Caution Hello

[Freesurfer] (no subject)

External Email - Use Caution Hello FreeSurfer Team, I recently messaged about running a longitudinal scan on a couple of images. The response told me to utilize "timepoints": For base processing, specify each timepoint with -tp <> (not the nii file). recon-all -base -tp -tp ..

[Freesurfer] (no subject)

External Email - Use Caution Dear Freesurfer Team, Greetings. My name is dr. Pukovisa Prawiroharjo, Sp.S(K), PhD. I am a lecturer and researcher at the Department of Neurology Faculty of Medicine Universitas Indonesia (UI) in Indonesia. I am pleased to inform you that we have bee

[Freesurfer] (no subject)

External Email - Use Caution Please unsubscribe me ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to w

[Freesurfer] (no subject)

External Email - Use Caution Hello, Is it feasible to get the password to access the FreeSurfer VirtualBox VM's FS 7 2 0 Ubuntu 18 04 06.ova.7z image? I sincerely appreciate it. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.ed

[Freesurfer] (no subject)

External Email - Use Caution Hi, I want to obtain the gyral height and the sulcal depth for every region of the aparc atlas. I know that in the file lh.sulc the positive values are the depth of the sulcus and the negative one are the height of the gyrus. How can I obtain separately

[Freesurfer] (no subject)

External Email - Use Caution behcetayyild...@gmail.com -- *Behçet Ayyıldız..* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is int

[Freesurfer] (no subject)

External Email - Use Caution Sorry if this is a repeat email from last night, but signal 9 can mean you ran out of memory.  You should try allocating more memory to the VM.. You could also try running the latest freesufer version = 7.3.2 which is compiled for Ubuntu 20 and you ca

[Freesurfer] (no subject)

External Email - Use Caution Hi, The FreeSurfer VM image needs a pass code to unarchive. Would you please send me the pass code? Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/l

[Freesurfer] (no subject)

External Email - Use Caution Hi, I try to do something like that, Would anyone help me -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: guelibbouc...@gmail.com __

Re: [Freesurfer] (no subject)

Not sure. I think those distortions are the surface folding back in on itself, so you may need more cuts. On 5/25/2022 9:26 AM, Alberto Pisoni wrote: External Email - Use Caution Hi all, I am trying to flatten a whole hemisphere, and i created the cut patch following the tutorials.

[Freesurfer] (no subject)

External Email - Use Caution Hi all, I am trying to flatten a whole hemisphere, and i created the cut patch following the tutorials. see the result here. https://secure-web.cisco.com/1yFIFkAQ7JVCxQ9XtdXA16rgidANEj5tq1VECDMPQ70qTME3GzCmOicwUAGbxA6C2o7Wi3CSEc6CbpZnD8HYT4PmTEB2s6XS9

Re: [Freesurfer] (no subject)

Just give freeview the path to whatever volume or surface you want to visualize Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Jabeur Mouna Sent: Wednesday, April 27, 2022 5:45 AM To: Freesurfer support list Subject: [Freesurfer] (no subject) External Email

[Freesurfer] (no subject)

External Email - Use Caution Hello, How can i import an image.nii from a folder different from /usr/local/freesurfer/7.2.0/subjects to visualise it with freeview ? Please! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] (no subject)

External Email - Use Caution Hello, Can you please clarify the following: Do we use subcortical QC rating for all subcortical measures such as accumbens as well measures such as total white matter volume. We do not use it for estimated total intracranial volume as this is accurat

Re: [Freesurfer] (no subject)

No, it should not On 6/22/2021 4:12 PM, miracle ozzoude wrote: External Email - Use Caution Hello All, I was wondering if the  Right/Left-Cerebral-White-Matter in the aparc+aseg.mgz contains WM hypointensities. mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats

[Freesurfer] (no subject)

External Email - Use Caution Hello All, I was wondering if the Right/Left-Cerebral-White-Matter in the aparc+aseg.mgz contains WM hypointensities. mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats --ctab FreeSurferColorLUT.txt Best, Paul

Re: [Freesurfer] (no subject)

External Email - Use Caution Hi Doug, I ran mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C groupdiff.mtx \--glmdir aseg.glmdir this created a folder aseg.glmdir which contains another folder groupdiff, where sig.ghm is, I then tried to visualise results using

Re: [Freesurfer] (no subject)

How did you create the sig.mgh that you are trying to overlay? On 5/28/2021 11:16 AM, Francisca Ferreira wrote: External Email - Use Caution Dear Experts, I have extracted subcortical vols corrected for intracranial vols using asegstats2table and I  ran mri_glmfit using the following

[Freesurfer] (no subject)

External Email - Use Caution Dear Experts, I have extracted subcortical vols corrected for intracranial vols using asegstats2table and I ran mri_glmfit using the following command mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C groupdiff.mtx \--glmdir aseg.glm

[Freesurfer] (no subject)

External Email - Use Caution Hello, I am running into errors when running segmentHA_T2.sh ${subj} /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1 Approximately 10% of my subjects are being processed but for some reason, the majority fail to execute. Here is

[Freesurfer] (no subject)

External Email - Use Caution Hi, Hope all are safe and well. Can anyone help me in finding any biomarker for Alzheimer's Disease or any guidance related to that? Waiting for response. Regards: Rahul Sharma Research Scholar 9827834360 *"Manners Maketh Man"* __

[Freesurfer] (no subject)

Dear Sir or Madam, I am not longer working with FreeSurfer so I would like to remove my subscription to the mailing list. Thank you, Laura smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer m

Re: [Freesurfer] (no subject)

No, you'll have to add it as a covariate. Or you can add --etiv when you run mris_preproc and it will divide the maps by the eTIV On 11/25/2020 3:23 PM, Sara Lyn wrote: External Email - Use Caution Hi Freesurfer experts, I'm doing a surface based volume analysis and wanted to know if t

[Freesurfer] (no subject)

External Email - Use Caution Hi Freesurfer experts, I'm doing a surface based volume analysis and wanted to know if there was a flag to regress out eTIV in the model. Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] (no subject)

External Email - Use Caution Windows 10 版のメール

Re: [Freesurfer] (no subject)

Try this instead aparcstats2table --hemi lh  --subjects subj10 --parc aparc.a2009s  --meas meancurv --tablefile /home/team33/ aparcstats.txt On 11/3/2020 12:20 PM, saman fouladi wrote: External Email - Use Caution hi I run in linux command: ""

Re: [Freesurfer] (no subject)

:24 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] (no subject) External Email - Use Caution hi I run in linux command: """""""""""""""""""""""&qu

[Freesurfer] (no subject)

External Email - Use Caution hi I run in linux command:""" aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj10/stats --parc aparc.a2009s  --meas meancurv --tablefile /home/team33/ aparcstats.txt"

[Freesurfer] (no subject)

External Email - Use Caution hi I was running several  putty windows for recond-all MRI pictures. Some putty were inactived during running. How can I activate them? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

Re: [Freesurfer] (no subject)

Sorry, that is not a question for us but rather for your local sys admin From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of saman fouladi Sent: Friday, October 23, 2020 6:52 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] (no subject) External Email - Use Caution hi

Re: [Freesurfer] (no subject)

Can you run recon-all again with -debug as the first argument? Send me the command line and all the terminal output On 7/9/2020 2:10 PM, Peka Savayan wrote: External Email - Use Caution The file that I sent you is the recon-all.log file. If copying file 'RB_all_2008-03-26.gca' from

Re: [Freesurfer] (no subject)

External Email - Use Caution The file that I sent you is the recon-all.log file. If copying file 'RB_all_2008-03-26.gca' from another FS version to directory /freesurfer-7.1.0/average will solve my problem? On Thu, Jul 9, 2020 at 12:30 PM Douglas N. Greve wrote: > Can you

Re: [Freesurfer] (no subject)

Can you send the recon-all.log file? On 7/9/2020 1:25 PM, Peka Savayan wrote: External Email - Use Caution I can open it. Can you? No permission required to my knowledge. On Thu, Jul 9, 2020 at 11:53 AM Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: Do you have read pe

Re: [Freesurfer] (no subject)

External Email - Use Caution I can open it. Can you? No permission required to my knowledge. On Thu, Jul 9, 2020 at 11:53 AM Douglas N. Greve wrote: > Do you have read permission to it? > > On 7/8/2020 2:25 PM, Peka Savayan wrote: > > External Email - Use Caution > Yes.

Re: [Freesurfer] (no subject)

Do you have read permission to it? On 7/8/2020 2:25 PM, Peka Savayan wrote: External Email - Use Caution Yes. On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: Does that file exist? On 7/7/2020 8:59 AM, Peka Savayan wrote:   

Re: [Freesurfer] (no subject)

External Email - Use Caution Yes. On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve wrote: > Does that file exist? > > On 7/7/2020 8:59 AM, Peka Savayan wrote: > > External Email - Use Caution > Dear experts, > > I try to run recon-all using FS 7.1.0 on a cluster with OS

Re: [Freesurfer] (no subject)

Does that file exist? On 7/7/2020 8:59 AM, Peka Savayan wrote: External Email - Use Caution Dear experts, I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6. I got the recon-all.log error message: ERROR: cannot find /share/apps/freesurfer-7.1.0/average/RB_all_2008-0

[Freesurfer] (no subject)

External Email - Use Caution Dear experts, I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6. I got the recon-all.log error message: ERROR: cannot find /share/apps/freesurfer-7.1.0/average/RB_all_2008-03-26.gca Thanks for your help. Sincerely, Peka -- Peka Ch

Re: [Freesurfer] (No Subject)

External Email - Use Caution is there a way to visualize the changes in thickness, area, and volume between the 2 timepoints (cortical and subcortical)? I was under the impression that running mri_preproc would aloow me to visualize change in cortical thickness bt the 2 timepoin

Re: [Freesurfer] (No Subject)

For thickness, you can look at the difference (or percent difference). You would use freeview (or tksurferfv, which is a frontend for freeview). When you run mris_preproc, you can specify that you want it to compute the (percent) difference, or you can do it with the multi-frame output of mris_

Re: [Freesurfer] (No Subject)

Oh, right. You only have one data point (the difference) and you are computing one parameter (the mean), so you have 0 DOF. If you only have one data point, there are not statistical tests you can do On 5/1/2020 3:34 AM, KennethSPrice wrote: External Email - Use Caution In the FSGD

Re: [Freesurfer] (No Subject)

External Email - Use Caution In the FSGD file I have one subject pair (timepoint 1 and timepoint 2), and it is the only group. However, I removed --fsgd and replaced it with --osgm upon your reccomendation, and am still getting the error. I am also having an issue visualizing th

Re: [Freesurfer] (No Subject)

how many subjects are there in your fsgd? How many groups in your fsgd file? Also, you should not use --osgm and --fsgd On 4/30/2020 1:09 PM, KennethSPrice wrote: External Email - Use Caution Hello Freesurfer friends! I'm going through the "paired analysis" tutorial and am running in

[Freesurfer] (No Subject)

External Email - Use Caution Hello Freesurfer friends! I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit I ran mris_prep

Re: [Freesurfer] (no subject)

the minimal compiled > distribution is less than 2GB. > > Andrew > > > > *From: * on behalf of Ерохин > Александр > *Reply-To: *Ерохин Александр , FS Help < > freesurfer@nmr.mgh.harvard.edu> > *Date: *Wednesday, April 22, 2020 at 12:35 PM > *To: *FS He

Re: [Freesurfer] (no subject)

I don’t have an exact number, but I believe the minimal compiled distribution is less than 2GB. Andrew From: on behalf of Ерохин Александр Reply-To: Ерохин Александр , FS Help Date: Wednesday, April 22, 2020 at 12:35 PM To: FS Help Subject: Re: [Freesurfer] (no subject) External

Re: [Freesurfer] (no subject)

consuming… >  >Hope that helps, >Andrew Hoopes >  >From: < freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Ерохин >Александр < erohin_...@mail.ru > >Reply-To: Ерохин Александр < erohin_...@mail.ru >, FS Help < >freesurfer@nmr.mgh.harvard.edu > >

Re: [Freesurfer] (no subject)

more time consuming… Hope that helps, Andrew Hoopes From: on behalf of Ерохин Александр Reply-To: Ерохин Александр , FS Help Date: Sunday, April 19, 2020 at 1:49 PM To: FS Help Subject: [Freesurfer] (no subject) External Email - Use Caution Hello together, The FreeSurfer

[Freesurfer] (no subject)

External Email - Use Caution Hello together,   The FreeSurfer distribution takes 10G of the disk space in my local installation. It has numerous tools, but it’s not modular, or at lest it’s very hard to tell boundaries between modules.   E.g. /bin folder contains around 860 exec

Re: [Freesurfer] (no subject)

External Email - Use Caution Thank you so much. I shall modify my other scripts then. Peng On Mon, 6 Apr 2020 at 16:59, Ruopeng Wang wrote: > I don’t think look up table works with negative indices. It was mainly > designed for label volumes. > > Ruopeng > > On Apr 6, 2020, at

Re: [Freesurfer] (no subject)

I don’t think look up table works with negative indices. It was mainly designed for label volumes. Ruopeng > On Apr 6, 2020, at 10:35 AM, Peng Liu wrote: > > External Email - Use Caution > > > Hi Ruopeng, > > Thank you for your reply. > > I have also tried NIH and JET, but

Re: [Freesurfer] (no subject)

External Email - Use Caution Hi Ruopeng, Thank you for your reply. I have also tried NIH and JET, but with negative scale, the entire image will turn into one same color as if there is some error. Meanwhile the reason of me trying to create .lut map is because I want five colour

Re: [Freesurfer] (no subject)

Hi Peng, Your lookup table only contains indices between 0 to 6. In any case I would not use look up table to display negative scales. Have you tried any other color maps like JET or NIH which has more colors? Best, Ruopeng > On Apr 6, 2020, at 6:30 AM, Peng Liu wrote: > > External E

[Freesurfer] (no subject)

External Email - Use Caution Dear Freesurfer experts, I am trying to customize a colour map of my own, with five colours and scale from -12.5 to 12.5, since when using Heat (with default options), the scale is correct but it is shown in only four colours. However after I created

Re: [Freesurfer] (no subject)

It is is really bright there, try putting a few control points in WM (make sure they are in WM) On 3/3/20 12:30 PM, Laboratorio de Neurociencia Funcional wrote: > > External Email - Use Caution > > Dear Freesurfeer experts, > After running the recon-all in one of my subjets, part of the t

[Freesurfer] (no subject)

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all in one of my subjets, part of the temporal lobe was partially excluded. Then, I tried to use the watershed algorithm to be less agressive in the skull stripping as follows: recon-all -skullstrip -w

[Freesurfer] (no subject)

External Email - Use Caution Hi Eugenio - Hope you are well. I am trying to extract the HSF from a group of processed brains. Previously I used the command: quantifyHippocampalSubfields.sh 195950 HSF_Cannabis Has this changed? If so what is the new command? Thanks, Alan -- *

[Freesurfer] (no subject)

External Email - Use Caution Hello Phillip, If you run the following command on that file - which is from the 6.0.0 freesurfer release, $ file /Applications/freesurfer/tktools/tkregister2.bin I think you will see that it reports it is a i386 binary - which is 32 bit - and cannot

Re: [Freesurfer] (no subject)

I'm guessing that the fragments might cause problems later either in gtmseg as a hard failure or in gtmpvc as an ill-conditioned matrix. But you can try it out:) On 1/11/2020 6:04 PM, Boris Rauchmann wrote: External Email - Use Caution Thanks, that solution seems to work finally. I jus

Re: [Freesurfer] (no subject)

External Email - Use Caution Thanks, that solution seems to work finally. I just ignored the remaining voxels labeled according to the standard aseg scheme and proceeded with the the PET analysis and the combined LUT. I will ignore the remaining fragment labels from the original

Re: [Freesurfer] (no subject)

On 1/8/2020 10:17 AM, Boris Rauchmann wrote: External Email - Use Caution Ok. i figured it out. The problem was just that you can not specify the file type - so .mgz in BN_Atlas_subcotex.mgz was actually the problem. Ah, ok. This is actually fixed in our development version. Now I ru

Re: [Freesurfer] (no subject)

External Email - Use Caution Ok. i figured it out. The problem was just that you can not specify the file type - so .mgz in BN_Atlas_subcotex.mgz was actually the problem. Now I run in a new issue: gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz --ctx-annot BN

Re: [Freesurfer] (no subject)

Are you sure you have permission to view that file? On 1/6/20 5:01 PM, Boris Rauchmann wrote: > External Email - Use Caution > > I’m sure just double checked it. I don’t know what’s wrong here. > > Von meinem iPhone gesendet > >>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. >>

Re: [Freesurfer] (no subject)

External Email - Use Caution I’m sure just double checked it. I don’t know what’s wrong here. Von meinem iPhone gesendet >> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. >> : > This is not making any sense to me. Are you sure you are in > $SUBJECTS_DIR/1122/mri when

Re: [Freesurfer] (no subject)

This is not making any sense to me. Are you sure you are in $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that BN_Atlas_subcotex.mgz is in the same folder? On 1/3/20 3:07 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > Thank you for testing it. As be

Re: [Freesurfer] (no subject)

External Email - Use Caution Thank you for testing it. As before I get the same error message. Do you know what I´m doing wrong here? Best, Boris MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR

Re: [Freesurfer] (no subject)

OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you try this command again? On 12/12/2019 11:57 AM, Boris Rauchmann wrote: External Email - Use Caution My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcot

Re: [Freesurfer] (no subject)

External Email - Use Caution Dear Douglas, I uploaded two files: 1122.tar.gz is the sample subject and BN_Atlas_freesurfer.tar.gz this is the Atlas I want use for the cortical and subcortical parcellation/segmentation. Thank you so much, Boris > Am 02.01.2020 um 17:06 schrieb

Re: [Freesurfer] (no subject)

Can you send me the subject data following these steps? From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no

Re: [Freesurfer] (no subject)

OK, I'm still at a loss. The one suspicious thing is that it only took a few min to run. So you have never looked at that volume? What is in the atlas? On 12/16/2019 3:42 PM, Boris Rauchmann wrote: External Email - Use Caution This is the log when I´m creating this file: Boriss-MacBook

Re: [Freesurfer] (no subject)

sorry, my fault. That was for someone else On Mon, 16 Dec 2019, Boris Rauchmann wrote: External Email - Use Caution This is the log when I´m creating this file: Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri

Re: [Freesurfer] (no subject)

to summarize, I want a warp that: foreach subject compute warp based on curvature apply warp to a functional overlay add that functional overlay to avg return (tf.reduce_mean(tf.square(avg))) make sense? So maximizing the mean squared average acivation On Mon, 16 Dec 2019, Boris Rau

Re: [Freesurfer] (no subject)

External Email - Use Caution This is the log when I´m creating this file: Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_

Re: [Freesurfer] (no subject)

External Email - Use Caution Thanks, it was created using: mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz Best, Boris > Am 16.12.2019 um 21:12 schri

Re: [Freesurfer] (no subject)

There is something weird about that file. How was it created? doug ps. Please include previous correspondence in the email On 12/16/19 1:12 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz > mghRead(/Users/boris/Des

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External Email - Use Caution Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): could not open file > Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. > : > > mri_info N_Atlas_subcotex.

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OK, now I'm really confused. Try this mri_info N_Atlas_subcotex.mgz On 12/14/19 3:04 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > Here the results: > > > pwd: > /Users/boris/Desktop/MirLIND_test/1122/mri > > ls -l BN_Atlas_subcotex.mgz: > -rwxrwxrwx 1 boris  staff  3701

[Freesurfer] (no subject)

External Email - Use Caution Hi experts, We are doing the segmentation of the subfields of the hippocampal and amygdala subfields, brainstem subestructures and thalamic nuclei. When we used segmentHA_T1.sh and segmentThalamicNuclei.sh, 'Command not found' appears. On the other ha

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External Email - Use Caution Here the results: pwd: /Users/boris/Desktop/MirLIND_test/1122/mri ls -l BN_Atlas_subcotex.mgz: -rwxrwxrwx 1 boris staff 37013 13 Aug 23:30 BN_Atlas_subcotex.mgz Best, Boris > Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D. > : > > pwd _

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ok, this is very strange to me. Can you send the result of these two commands pwd and ls -l BN_Atlas_subcotex.mgz On 12/13/2019 2:22 AM, Boris Rauchmann wrote: External Email - Use Caution yes to both. I always get the error ERROR: cannot find aseg... On Fri, Dec 13, 2019 at 12:58

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External Email - Use Caution yes to both. I always get the error ERROR: cannot find aseg... On Fri, Dec 13, 2019 at 12:58 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that > folder? > > On 12/12/1

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Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that folder? On 12/12/19 12:57 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg > BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz > SUBJEC

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External Email - Use Caution My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz SUBJECTS_DIR /Users/boris/Desktop/mydir subject 1122 outvol aparc+BN_Atlas_subcotex.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading l

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Hi Boris can you send us the full command line and screen output of the commands that are failing? cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote: External Email - Use Caution Thanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_s

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External Email - Use Caution Thanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz The file BN_Atlas_subcotex.mgz was create

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What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your subcortical ROIs added? If so, you can try merging it with the aparc, eg, mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz Then use aparc+BN_Atlas_subcotex.mgz as input to xcere

[Freesurfer] (no subject)

External Email - Use Caution Yes, you can disable the gatekeeper security software and allow software to be installed anywhere.  This may not be the best choice for everyone if you prefer to have this security (or do not have sudo privs).   Anyway, we will endeavor to not requir

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External Email - Use Caution In this example tried it with only the subcortical segmentations from my atlas. Please find the logfile attached. It gives me back: "tissue type is not set" but I set it to 2 in the LUT.txt In principle look the following commands right to you? xcereb

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Can you send the log file for each of the gtmseg runs? On 11/26/2019 1:09 PM, Boris Rauchmann wrote: External Email - Use Caution Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical structures. I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_lab

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