[Freesurfer] Problems Freesurfer 5.3 License on Ubuntu 20

Hello, We have a problem with our license for Freesurfer 5.3 on Ubuntu 20. Previously we used the same license on our old computing node on CentOS 7 without any problems. On our new node we get this message: ERROR: Invalid FreeSurfer license key found in license file /opt/apps/freesurfer

[Freesurfer] Problems with identifying fornix using TRACULA

External Email - Use Caution Hi all, We recently processed our DWI data (school-aged children) using the updated version of TRACULA (Freesurfer 7.2). We were mainly interested in using this version because of the addition of the fornix to the atlas. After processing the data, we n

Re: [Freesurfer] Problems with recon for manually fixed

ed, 26 Jan 2022 16:43:44 -0500 > From: "Douglas N. Greve" > Subject: Re: [Freesurfer] Problems with recon for manually fixed > Talairach > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <8e0752c5-13fa-755e-c416-4253ce504...@mgh.harvard.edu> > Content-Type:

Re: [Freesurfer] Problems with recon for manually fixed Talairach

what version of FS are you using? On 1/21/2022 2:21 PM, Goeckner, Bryna wrote: External Email - Use Caution Hi, I am trying to decide how to proceed after manually updating a talairach since various ways I’ve tried the recon process give me different results. Our group used Freesu

Re: [Freesurfer] problems about freesurfer7 with T2pial flag

That appears to be a bug in 7.1.1. As long as the surfaces are ok, you don't need to worry. On 2/22/2021 11:57 PM, Yijun Chen wrote: External Email - Use Caution Hi freesurfer experts: I encountered a problem about freesurfer 7 with the T2pial flag. when I use the freesurfer 6 — reco

[Freesurfer] problems about freesurfer7 with T2pial flag

External Email - Use Caution Hi freesurfer experts: I encountered a problem about freesurfer 7 with the T2pial flag. when I use the freesurfer 6 — recon-all -all -i -s -T2 -T2pial, the resulting T2.mgz is skull-stripped. however, when I switch to the freesurfer 7, the resulting T2

Re: [Freesurfer] problems with brainmask.mgz and wm.mgz files

Can you send a pic of the brain before and after skull strip? On 8/24/2020 12:00 PM, Dalton Bermudez wrote: External Email - Use Caution For some reason when I ran the recon-all command it generated a brainmask.mgz file which excluded part of the right hemisphere and a wm.mgz which d

Re: [Freesurfer] Problems with freesurfer 7.1.0 and MacOS

>>> Andrew >>> >>> >>> From: >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Angela Favaro >>> mailto:angela.fav...@unipd.it>> >>> Reply-To: FS Help >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>

Re: [Freesurfer] Problems with freesurfer 7.1.0

esurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Angela Favaro >> mailto:angela.fav...@unipd.it>> >> Reply-To: FS Help > <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Date: Wednesday, May 27, 2020 at 4:27 PM >> To: FS Help > <mailto:freesurf

Re: [Freesurfer] Problems with freesurfer 7.1.0

r/freesurfer/dev/scripts/rca-long-tp-init> > -o rca-long-tp-init > sudo chmod +x rca-long-tp-init > > Best > Andrew > > > From: on behalf of Angela Favaro > > Reply-To: FS Help > Date: Wednesday, May 27, 2020 at 4:27 PM > To: FS Help > Subje

Re: [Freesurfer] Problems with freesurfer 7.1.0

/freesurfer/freesurfer/dev/scripts/rca-long-tp-init -o rca-long-tp-init sudo chmod +x rca-long-tp-init Best Andrew From: on behalf of Angela Favaro Reply-To: FS Help Date: Wednesday, May 27, 2020 at 4:27 PM To: FS Help Subject: [Freesurfer] Problems with freesurfer 7.1.0 External Email

[Freesurfer] Problems with freesurfer 7.1.0

External Email - Use Caution Dear Freesurfer experts, I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS Catalina. I found 2 main problems 1. About a 10% of cases failed at the segmentation stage during the recon-all processing (I uploaded one of these

Re: [Freesurfer] Problems about registration and tksurfer

Try using mri_vol2surf to sample your fMRI onto the surface, then load it as a surface overlay in freeview On 11/29/2019 3:35 AM, 朱青 wrote: External Email - Use Caution Dear madam or sir, I'm a student in China who use the Freesurfer to analyse my fMRI data and overlay some results

Re: [Freesurfer] problems compiling Freesurfer

External Email - Use Caution ​ Hello Jorge, You can download a tar archive of the pre-built 3rd party packages with the following command, curl -O http://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/centos7-packages.tar.gz - and the versions of the contained packages i

[Freesurfer] problems compiling Freesurfer

External Email - Use Caution Hi All, IM compiling freesurfer, after many bumps reached a point i havent figured out how to proceed. My setup: Centos7 GCC 4.8.5 Freesurfer 6.0.0 Dependencies as in /usr/pubsw/packages/ - KWWWidgets : CVS-vtk560 - petsc : 2.3.3-p13 - mni 1.5 - t

Re: [Freesurfer] Problems with recon-all -s soft and hard fallures

External Email - Use Caution Dear Greve, Please can you let me know if you got the two folders of data I sent you? Best regards Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaa

Re: [Freesurfer] Problems with recon-all -s soft and hard fallures

External Email - Use Caution Hi Bruce, I dragged into the folder "incoming" a folder called "sub025" (soft failure) for the first problem and a folder called "sub-31" (hard failure) for the second problem Can you see them? Thanks Looking forward to hear from you Ileana Ilean

Re: [Freesurfer] Problems with recon-all -s soft and hard fallures

Hi Ileana you use "anonymous" for the user name and your email for the password I believe. cheers Bruce On Wed, 17 Apr 2019, Camerino, .I.L. (Ileana) wrote: External Email - Use Caution Hi Greve, Thank you very much for your reply. How do I add data to the link you sent me? When I

Re: [Freesurfer] Problems with recon-all -s soft and hard fallures

External Email - Use Caution Hi Greve, Thank you very much for your reply. How do I add data to the link you sent me? When I click on it, a pop up appears and I need to fill in a password to connect to the server. Which password should I use? If I copy the link on a browser,

Re: [Freesurfer] Problems with recon-all -s soft and hard fallures

Unfortunately, it usually means that you need to go in and manually fix the problems that you are seeing. Probably the best thing is to look at the aseg.presurf.mgz to see how the WM lesions are getting labeled. You may have to go in an label them manually. Can you upload a case or two here ftp

Re: [Freesurfer] problems with Freeview

External Email - Use Caution Hi Ruopeng, I have just uploaded the files. Thank you for your help. Best, Jose El jue., 31 ene. 2019 a las 17:32, Ruopeng Wang () escribió: > You can send via filedrop here: > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > Use rpwang as recipien

Re: [Freesurfer] problems with Freeview

You can send via filedrop here: https://gate.nmr.mgh.harvard.edu/filedrop2/ Use rpwang as recipient. Thanks. On 1/31/19 11:29 AM, Laboratorio de Neurociencia Funcional wrote: Please let me know how to send you these files. El jue., 31 ene. 2019 a las 17:19, Ruopeng Wang (mailto:rpw...@nmr.mg

Re: [Freesurfer] problems with Freeview

External Email - Use Caution Please let me know how to send you these files. El jue., 31 ene. 2019 a las 17:19, Ruopeng Wang () escribió: > Can you send us a T1.mgz file along with a lh.white file that do not align > when loaded in freeview? > On 1/31/19 10:47 AM, Laboratorio de

Re: [Freesurfer] problems with Freeview

Can you send us a T1.mgz file along with a lh.white file that do not align when loaded in freeview? On 1/31/19 10:47 AM, Laboratorio de Neurociencia Funcional wrote: No, we didn't have the same problem neither with Freesurfer 6.0 or with the development Freesurfer version. The problem only aris

Re: [Freesurfer] problems with Freeview

External Email - Use Caution No, we didn't have the same problem neither with Freesurfer 6.0 or with the development Freesurfer version. The problem only arises when we display FS images with Freeview using Freesurfer (6.0 or development version). For that reason, I asked you about

Re: [Freesurfer] problems with Freeview

That’s unlikely. Did FS 6.0 have the same problem? > On Jan 31, 2019, at 9:59 AM, Laboratorio de Neurociencia Funcional > wrote: > > External Email - Use Caution > > > Hi Ruopeng, > > we have tried these commands with Bert and with different datasets and the > problem persi

Re: [Freesurfer] problems with Freeview

External Email - Use Caution Hi Ruopeng, we have tried these commands with Bert and with different datasets and the problem persists. Could the problem be related to the way that we have installed Freeview or something wrong between Freeview and the Ubuntu version that we are usin

Re: [Freesurfer] problems with Freeview

Your screenshot appears to be from burt data but I assume it was loaded with similar commands. I could not replicate the displacement with burt data. Would it be possible to send me T1.mgz and lh.white file from this OSM_0 subject? Thanks, Ruopeng > On Jan 31, 2019, at 9:18 AM, Laboratorio de

Re: [Freesurfer] problems with Freeview

External Email - Use Caution Sure, commands are copied below: *File > Run Command* *-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz* *-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz* *-**f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow* *-f /u

Re: [Freesurfer] problems with Freeview

Can you share the freeview command you run to load the these data? Ruopeng > On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional > wrote: > > External Email - Use Caution > > > Dear Freesurfers, > > we have installed the updated Freeview version in the develop

[Freesurfer] Problems with GM segmentation

External Email - Use Caution Dear Free Surfer team, I few days ago I sent you personally the dicom files as well as the mask of the lesion you asked me for as I am having problems with GM segmentation. I would greatly appreciate if you could help me with this issue and tell me how

Re: [Freesurfer] problems with bbregister's output image

You have effectively applied the registration twice, once when you ran bbregister to get the output and once when you ran tkregister2 with --reg. Try that tkrister2 command with func.nii.gz as the --mov On 1/21/19 6:35 PM, Sam W. wrote: > > External Email - Use Caution > > Hello, > > I h

[Freesurfer] problems with bbregister's output image

External Email - Use Caution Hello, I have registered example_func.nii.gz to the anatomical image using bbregister and then I looked at the registered file with tkregister2. $ bbregister --bold --lta reg.lta --mov example_func.nii.gz --s sub001 --o f-in-anat.nii.gz $ tkregister2

Re: [Freesurfer] Problems with GM segmentation -- How to solve it

External Email - Use Caution Hi Bruce, Already sent: ftp> put 013.tar.gz local: 013.tar.gz remote: 013.tar.gz 200 PORT command successful. Consider using PASV. 150 Ok to send data. 226 Transfer complete. 223104380 bytes sent in 808.49 secs (269.4852 kB/s) ftp> On Wed, Dec 12, 20

Re: [Freesurfer] Problems with GM segmentation -- How to solve it

External Email - Use Caution Hi Bruce, Thank you for your reply. I am sending now a file called 013.tar.gz via ftp. And this is not the worst...there are other with more regions that have not been considered in the segmentation process. I would like to know how could I cope with G

Re: [Freesurfer] Problems with GM segmentation -- How to solve it

Hi Rosalia if you upload an example with voxel coordinates of where you see problems we will take a look cheers Bruce On Tue, 11 Dec 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Dear Free Surfer team and Bruce, I have been doing well editing the skull s

[Freesurfer] Problems with GM segmentation -- How to solve it

External Email - Use Caution Dear Free Surfer team and Bruce, I have been doing well editing the skull stripping, and using control points to improve white matter segmentation. Furthermore, the few participants I had problems with due to large ventricles were solved using the flag

Re: [Freesurfer] Problems with skull stripping

External Email - Use Caution Hi Bruce, I will send it you once I am in the lab. In relation to the tutorials, I know that there are tutorials and pdf documentation I have been consulting. But, just to start with editing, it would be helpful to see how another person is doing it in

Re: [Freesurfer] Problems with skull stripping

Hi Rosalia there are some tutorials on our website. And can you send us the recon-all.log where you have put a new brainmask.mgz into the subject's dir and it gets overwritten? That shouldn't happen thanks Bruce On Thu, 15 Nov 2018, Rosalia Dacosta Aguayo wrote: External Email -

Re: [Freesurfer] Problems with skull stripping

External Email - Use Caution HI Bruce, I have to run recon-all -autorecon1, then substitute the brainmask for my brainmask, changing the brainmask from FS to brainmask.original.FS and labelling my betted image brainmask.mgz and then run recon-all -autorecon2 becuase if I do as you

Re: [Freesurfer] Problems with skull stripping

Hi Rosalia yes, editing and rerunning recon-all should work. Or update the brainmask.mgz with your own version if you want. We should detect that and retain it. cheers Bruce On Wed, 14 Nov 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Dear Free Surfe

[Freesurfer] Problems with skull stripping

External Email - Use Caution Dear Free Surfer team, Sorry for double posting but I would like to explain well so it will be easier to understand what I am looking for. 1. I have run recon-all -all in a participant 2. The skull stripped image has skull and dura behind. 3. I can m

[Freesurfer] problems concerning mris_prepoc

External Email - Use CautionDear Sir or Madam,   I am currently trying to run a group analysis on FreeSurfer. After having created a FSGD-File I tried mris_prepoc. As a command I use   mris_preproc --fsgd FSGD_File_Aggression.fsgd --cache-in thickness.fwhm10.fsaverage --target

Re: [Freesurfer] Problems to run -autorecon2

Hi Rosalia once you have imported the data for a subject with -i , you shouldn't specify it for subsequent analyses cheers Bruce On Fri, 19 Oct 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Dear FreeSurfer team, I am trying to run recon -all -autoreco

Re: [Freesurfer] Problems to run -autorecon2

esurfer-boun...@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta > Aguayo > *Gesendet:* Freitag, 19. Oktober 2018 14:40 > *An:* Freesurfer support list > *Betreff:* Re: [Freesurfer] Problems to run -autorecon2 > > > > *External Email - Use Caution* >

Re: [Freesurfer] Problems to run -autorecon2

Gesendet: Freitag, 19. Oktober 2018 14:40 An: Freesurfer support list Betreff: Re: [Freesurfer] Problems to run -autorecon2 External Email - Use Caution Dear Falk, Thank you very much. Once last question: what would happen if I did run -autorecon1 without the flags: -qcache -openmp 8

Re: [Freesurfer] Problems to run -autorecon2

essing your data, as this flag tells > FreeSurfer to create a new subject folder (which already exists and > therefore give an error). > > > > Best, > > Falk > > > > > > *Von:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh

Re: [Freesurfer] Problems to run -autorecon2

Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Rosalia Dacosta Aguayo Gesendet: Freitag, 19. Oktober 2018 14:10 An: Freesurfer support list Betreff: Re: [Freesurfer] Problems to run -autorecon2 External Email - Use Caution

Re: [Freesurfer] Problems to run -autorecon2

r.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta > Aguayo > *Gesendet:* Freitag, 19. Oktober 2018 11:11 > *An:* Freesurfer support list > *Betreff:* [Freesurfer] Problems to run -autorecon2 > > > > *External Email - Use Caution* > > Dear FreeSurfer team,

Re: [Freesurfer] Problems to run -autorecon2

: [Freesurfer] Problems to run -autorecon2 External Email - Use Caution Dear FreeSurfer team, I am trying to run recon -all -autorecon2 using the following command line: recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2 It is

[Freesurfer] Problems running the three steps from Free Surfer separately

External Email - Use Caution Dear Free Surfer team, I keep trying to run -autorecon2 but it seems that I should have run recon -all -all instead as I am having problems with the names of my subjects and the same error appears once and again and I do not know how I should do it so

[Freesurfer] Problems to run -autorecon2

External Email - Use Caution Dear FreeSurfer team, I am trying to run recon -all -autorecon2 using the following command line: *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2* It is the same command I used yesterday t

Re: [Freesurfer] Problems setting the directory

Hi Rosalia that you would do outside of FreeSurfer, probably with a shell script. I typically make a scripts dir under SUBJECTS_DIR and put a file names subjects.csh that creates an env variable listing the subjects and setting the SUBJECTS_DIR, then write scripts that source it and run things

Re: [Freesurfer] Problems setting the directory

External Email - Use Caution Thank you a lot Bruce. Just one more question. If I would like to run all the participants. where should I include the subject.list? Regards, Rosalia On Thu, Oct 18, 2018 at 7:56 PM Bruce Fischl wrote: > yes, you can do that. If you run recon-all thr

Re: [Freesurfer] Problems setting the directory

yes, you can do that. If you run recon-all through the skill stripping, then replace the brainmask.mgz with yours generated by bet, we should detect that and retain it for further processing cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Cautio

Re: [Freesurfer] Problems setting the directory

External Email - Use Caution Yes, you are right. I saw the error. I have been running one of the participants and here it is the report.log. Also, because these kind of participants are special, I used some bet parameters to run the skull-stripping. This is the main reason why I di

Re: [Freesurfer] Problems setting the directory

Hi Rosalia -i must point to a file that you want to import, usually a single dicom file in the correct (e.g. mprage) series. cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Hi Bruce, There is not recon-all.log. The full comman

Re: [Freesurfer] Problems setting the directory

External Email - Use Caution Hi Bruce, There is not recon-all.log. The full command line is: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1* *ERROR

Re: [Freesurfer] Problems setting the directory

Hi Rosalia can you send us the full command line, screen output and recon-all.log? In the arrangement you show below it would be: recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i -all cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution

Re: [Freesurfer] Problems setting the directory

External Email - Use Caution Hi Bruce, Thank you very much for answering my questions. This is how I have organized my subject_dir for one subject so you can see better. It is still not working. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls FOLDERS S_01

Re: [Freesurfer] Problems setting the directory

Hi Rosalia you either need to give recon-all an input file (or more than one) with the -i switch, or create the subject directory tree under SUBJECTS_DIR for that subject, and put a file named 001.mgz in the mri/orig subdir. Note you can also specify SUBJECTS_DIR explicitly on the recon-all co

[Freesurfer] Problems setting the directory

External Email - Use Caution Dear Free Surfer team, Surely this is a basic question but I am having a trouble setting the subjects_dir in my terminal and, as a result, any of the commands work. This is how I have my Free Surfer configurated in my computer: freesurfer-Li

[Freesurfer] Problems with thalami nuclei segmentation

External Email - Use Caution Hi list, 1- I have run the segmentThalamicNuclei.sh but .stats file has been not produced in any subjects. I have also try to re-run recon-all with dev version but fulling. 2 - Moreover, when I use the thalami segmentation as seed in FS-FAST I obt

[Freesurfer] Problems associated segmentation results of hippocampal subfields

External Email - Use Caution Dear All, I have a problem with the Freesurfer hippocampal longitudinal segmentation results , when i have done segmentation using following algorithm ( https://github.com/CobraLab/antsRegistration-MAGeT) with no anterior/posterior partitioning ( Head/

Re: [Freesurfer] Problems Extending the Pial Surface

External Email - Use Caution Hi Bruce, I sent you the whole directory if one subject un which we had some problems extending the pial surface. Se would like extend the pial surface without affect the wm boundary. Did you have a chance to review It? Thanks in advance, Cheers,

Re: [Freesurfer] Problems at exporting recon-all outputs

Hi Miguel I think in Christophe's atlas not all folds occur in all subjects. cheers Bruce On Sat, 5 May 2018, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Hi Freesurfer developers, After having executed the recon-all in several subjects I tried to exp

[Freesurfer] Problems at exporting recon-all outputs

External Email - Use Caution Hi Freesurfer developers, After having executed the recon-all in several subjects I tried to export all measures of the Destrieux atlas (area, volume, curvind, foldind, gauscurv, meancurv, thickness and thicknesstd) but I got an error because in some

Re: [Freesurfer] Problems Extending the Pial Surface

External Email - Use Caution Hi Bruce, I tried to upload the whole subject dir in the ftp site but i didn´t works. I send you the file in 7zip format trough a google drive link . I would know how can i extend the pial surface without affect the wm boundaries because the pial surf

Re: [Freesurfer] Problems Extending the Pial Surface

why don't you tar and gzip the whole subject dir and upload it to our ftp site and we will take a look cheers Bruce On Tue, 1 May 2018, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Hi Bruce, The problem is that the reconstruction of the pial surface is

Re: [Freesurfer] Problems Extending the Pial Surface

External Email - Use Caution Hi Bruce, The problem is that the reconstruction of the pial surface is incorrect. I tried to put control points on some voxels but did a wrong reconstruction because in this region there is no voxel with an intensity between 95-110. How can I improve

Re: [Freesurfer] Problems Extending the Pial Surface

that looks like a big temporal lobe bias field to me. Is the WM in the temporal lobes significantly darker than 110? I can't tell if some of the stuff in e.g. the left medial temporal lobe is WM or GM. Try putting some control points in regions where the intensity is in say [95, 110) and see if

Re: [Freesurfer] Problems Extending the Pial Surface

Hi Saum it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be

[Freesurfer] Problems Extending the Pial Surface

External Email - Use Caution Hi guys, I'm having some trouble extending the pial surface of my bm volume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without aff

Re: [Freesurfer] Problems displaying pial_lgi in dec

Sorry, qdec is not really being supported anymore. It is recommended that you run your group analysis through the command line stream (ie, mris_preproc, mris_fwhm to smooth, then mri_glmfit and mri_glmfit-sim). On 3/21/18 3:45 PM, Dusan Hirjak wrote: Dear Freesurfer Experts, I would like t

[Freesurfer] Problems displaying pial_lgi in dec

Dear Freesurfer Experts, I would like to display my results after running the LGI command on my subjects (via Freesurfer 6.0, MacOS Sierra). Although I created the .Qdecrc (text file) file with MEASURE1 = pial_lgi and put it in my home directory as well as in the folder where my study subjects

Re: [Freesurfer] Problems running LGI {Disarmed}

Dear Andrew, thank you very much! Yes, you were right! Now it works fine. best regards Dusan From: Hoopes, Andrew Sent: Tuesday, February 13, 2018 12:23 PM To: Freesurfer support list; Dusan Hirjak Subject: Re: [Freesurfer] Problems running LGI Hi Dusan

Re: [Freesurfer] Problems running LGI

Hi Dusan, I just remembered that this is probably due to SIP being enabled on your mac, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best, And

Re: [Freesurfer] Problems running LGI

Hi Dusan, I’ll take a look at this and get back to you soon. I think this issue is related to the matlab version. best Andrew On February 10, 2018 at 4:27:11 PM, Dusan Hirjak (dusanhir...@hotmail.com) wrote: Dear Freesurfer Experts, I am currently trying to

[Freesurfer] Problems running LGI

Dear Freesurfer Experts, I am currently trying to run LGI. I have the 2017b Matlab version, Mac OS Sierra and I already set up the freesurfer PATH in Matlab. However, I am getting the following error after starting recon all -s localGI : Dusans-MacBook-Pro:NSS_Analysis_01 dusan$ recon-all -s

Re: [Freesurfer] Problems transforming T1 to talairach

Try adding -oc 0 0 0 to the mri_convert command line On 2/2/18 7:27 AM, Helen Beaumont wrote: > I am using the command > mri_convert -at transforms/talairach.xfm brain.mgz brain_in_tal.nii.gz > > to convert a native-space skull-stripped T1 image to talairach space. I used > recon-all to generat

[Freesurfer] Problems transforming T1 to talairach

I am using the command mri_convert -at transforms/talairach.xfm brain.mgz brain_in_tal.nii.gz to convert a native-space skull-stripped T1 image to talairach space. I used recon-all to generate the transform matrix, and the segmentation and everything look good. But the T1_in_talairach image is

Re: [Freesurfer] Problems with FtpFileExchange

Hi Rosalia at that point you should just be able to type: put S_001.zip which should copy it to our ftp site. cheers Bruce On Wed, 22 Nov 2017, Rosalia Dacosta Aguayo wrote: Dear FreeSurfer Developers, I am having problems with FtpFileExchange. I am trying to upload a compressed file

[Freesurfer] Problems with FtpFileExchange

Dear FreeSurfer Developers, I am having problems with FtpFileExchange. I am trying to upload a compressed file Bruce asked me to upload and it seems I am missing something in the last point of the instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange *What I have done till now*:

Re: [Freesurfer] Problems when loading surface and mesh showing vertices

Dear Bruce, I am using FileDropv2.0... I hope you and all the members of the list can access into this subject. Thank you for your help in advance, Rosalia 2017-11-21 18:35 GMT+01:00 Rosalia Dacosta Aguayo : > Sorry Bruce, > > Here is the problem I wanted to avoid: > > freesurfer-Lin

Re: [Freesurfer] Problems when loading surface and mesh showing vertices

Sorry Bruce, I have sent it to your email directly...in order to avoid the process of uploading the data...because I am not familiar with it. Kind regards, Rosalia 2017-11-21 18:25 GMT+01:00 Rosalia Dacosta Aguayo : > Sorry Bruce, > > I prefer sending it to your email directly, then if you want

Re: [Freesurfer] Problems when loading surface and mesh showing vertices

tar and gzip the entire subject dir and upload it following these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo wrote:  Hi Bruce, Thank you for answering. Not, it is not a bug...in fact recon-all...-all had not problems

Re: [Freesurfer] Problems when loading surface and mesh showing vertices

Hi Bruce, Thank you for answering. Not, it is not a bug...in fact recon-all...-all had not problems. Just I was looking at the outputs...and as I am running FreeSurfer for my first time I wanted to ask about if this was a problem or I can go on Where I should upload the subject and which fi

Re: [Freesurfer] Problems when loading surface and mesh showing vertices

hmmm, that is odd looking. Can you upload that subject so we can see if it is just a display bug or not? On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo wrote: > Dear FreeSurfer Developers, > > I am checking the OutputData_freeview after running recon-all following your > tutorial: > https://surfer

[Freesurfer] Problems after running recon-all ...-qcache

Dear FreeSurfer Developers, I have run recon-all-qcache after reviewing the recon-all...-all outputs in freeview. I have been looking into: https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc Now it seems that I could have omitted the -qcache...and I am a bit lost with the examples sh

Re: [Freesurfer] problems of testing freesurfer

When setting SUBJECTS_DIR, you have to specify the actual path to the “test_subjects” directory that you created. "/path/to/test_subjects" isn’t a real path on your computer. In your case, the path might be something like "/Users/DannyDeng/test_subjects” In recon-all, the -i flag is used to des

Re: [Freesurfer] problems of testing freesurfer

Hi Andrew, I have followed your suggestion and the error pop up like this: Xues-MacBook-Air:~ DannyDeng$ mkdir test_subjects mkdir: test_subjects: File exists Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=/path/to/test_subjects Xues-MacBook-Air:~ DannyDeng$ cd${FREESURFER_HOME}/subjects/sampl

Re: [Freesurfer] problems of testing freesurfer

Hi Danny, The SUBJECTS_DIR variable defines the path to a directory where freesurfer recon data is stored for a particular study. When setting this path variable, you don’t need to include the <> brackets. After sourcing freesurfer, start by making a sample directory and defining your SUBJECTS

[Freesurfer] problems of testing freesurfer

Hi developers, I just installed the software and there are so many problems I wish to seek help from you when I tried “Test your freesurfer installation” on the website Example 2 I tried several commands as follow but all failed: 1. Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=<$FREESURF

[Freesurfer] problems with segmentHA_T1_long.sh

Hello, I ran a longitudinal analysis cortical structure in Freesurfer version 5.3. I'd now like to compute hippocampus subfields using the new beta version of the "Segmentation of hippocampal subfields and nuclei of the amygdala" tool (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfi

Re: [Freesurfer] problems with recon-all in 6.0

Not sure. First, let's make sure that the dicom can be converted with mri_convert 01001/0/2/1.dcm deleteme.mgh try that and let us know if it succeeds On 07/14/2017 04:13 AM, Lars M. Rimol wrote: > Hi, > > I'm trying to run recon-all in FreeSurfer 6.0 but I keep getting > error messages and s

[Freesurfer] problems with recon-all in 6.0

Hi, I'm trying to run recon-all in FreeSurfer 6.0 but I keep getting error messages and some strange behavior: ls 01001/0/2/ 100.dcm 106.dcm 111.dcm 117.dcm 122.dcm 128.dcm 133.dcm 139.dcm 144.dcm 14.dcm 155.dcm 160.dcm 166.dcm 171.dcm 17.dcm 22.dcm 28.dcm 33.dcm 39.dcm 44.dcm

Re: [Freesurfer] Problems changing automatic SUBJECTS_DIR file path

ubject: Re: [Freesurfer] Problems changing automatic SUBJECTS_DIR file path Hi Valerie, It looks like you might be using bash shell, in which case you should be using the 'export' command instead of setenv to change its value (note the difference in syntax): export SUBJECTS_DIR= Please note.

Re: [Freesurfer] Problems changing automatic SUBJECTS_DIR file path

Hi Valerie, It looks like you might be using bash shell, in which case you should be using the 'export' command instead of setenv to change its value (note the difference in syntax): export SUBJECTS_DIR= Please note... It looks like you are using a very old version of freesurfer. Freesurfe

[Freesurfer] Problems changing automatic SUBJECTS_DIR file path

Hi FreeSurfer Developers, I'm new to Linux as well as freesurfer and picking up with the program where an old lab assistant left off. He already installed the program and fsfast, but set the subjects directory using a file path unique to his user and I'm having trouble changing it. Calling up

Re: [Freesurfer] Problems with QDEC

On 08/05/2016 12:33 PM, Vikas Bandalli wrote: > Thank you Doug, > > I am very sorry I hadn't explained our subject considered for analysis. > The subjects group consists of Patients who are classified into > a.Those with Psychosis - Psychotic-pt > b. Those without Psychosis - Non-Psychotic-pt >

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