Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

ersity College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Jasmin > Alves > *Reply-To: *Freesurfer support list > *Date: *Wednesday, 11 July 2018 at 17:16 > *To: *Freesurfer support list >

Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

sure segmentSubjectT1_autoEstimateAlveusML works with this version of OS X. You may need to reinstall the application. Be sure to install any available updates for the application and OS X. Thanks, Jasmin On Wed, Jul 11, 2018 at 9:15 AM, Jasmin Alves wrote: > Hello Eugenio, > > Thank you for the rep

Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

ike pwd and dirname. Are these in your path? > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com >

[Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

o no avail. Version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c OS: X V 10.9.5 Thanks! Jasmin -- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list

Re: [Freesurfer] question about recon-all

the log that it wouldn't have finished > > > Bruce > > > On Thu, 1 Jun 2017, Jasmin Alves wrote: > > Hi Bruce, >> So it does not matter that the recon-all.done script never appeared in the >> script folder? Or that the isrunning.lh+rh script is still in

Re: [Freesurfer] question about recon-all

n get realiable thickness estimates off this kind of data, but you > should be able to do e.g. fMRI analysis. > > There were a bunch of big defects so the topology fixing took a lot longer > than usual, but it did complete > > cheers > Bruce > > > On Thu, 1 Jun 20

Re: [Freesurfer] question about recon-all

=DwIDaQ&c=clK7kQ > UTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHL > ug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_ooLOM&s=SWUWcgct6 > aIswjAqZt3RiFgjtOfIpqIKiryZ4Xu1aSM&e= > but at that point you might as well tar and gzip the entire subject dir > and up

[Freesurfer] question about recon-all

e? Or does FS6.0 possibly take longer to complete for some brains? Thanks, Jasmin -- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] repost aseg.mgz error

? > > On 08/12/2016 12:00 PM, Jasmin Alves wrote: > > Dear Freesurfer > > > > I encountered an error on the aseg mask for a participant, both > > hemispheres for the aseg appear on one hemisphere of the brain mask. > > > > I ran it a few times and I also u

[Freesurfer] repost aseg.mgz error

-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] hippocampus question

ung adult human brain: an MRI-based morphometric analysis. > Cereb. Cortex 4, 344–360 > > You can find the refs in our Neuron paper on whole-brain segmentation > > cheers > Bruce > > > On Mon, 8 Aug 2016, Jasmin Alves wrote: > > Dear Freesurfer, >> I have no

[Freesurfer] hippocampus question

includes as regional boundaries for the hippocampus. Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] question about aseg.mgz

lly check the aseg.mgz display *over* the norm.mgz to see if the > labels make sense w.r.t. the intensities. > > cheers > Bruce > On Sat, 2 Jul 2016, Jasmin Alves wrote: > > Dear Freesurfer support, >> I noticed in previous threads, people have inquired about how to check

[Freesurfer] question about aseg.mgz

will have to edit almost every voxel. Your suggestions would be greatly appreciated. Thanks, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list

[Freesurfer] aseg mask error

eg is being mapped onto one hemisphere. This is the case with two different mprage files. I have attached a screenshot. I am not quite sure how to fix this. Is it something I should fix using TKMEDIT? Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program Universi

Re: [Freesurfer] DTI error

x27;d check if you are indeed typing a > plain "-c". > > Best, > a.y > > > On Wed, 25 May 2016, Jasmin Alves wrote: > > Hi Anastasia, >> I am still receiving the following error message when I run a different >> participant doing, trac-all -path –c >&g

Re: [Freesurfer] DTI error

, May 22, 2016 at 9:07 PM, Jasmin Alves wrote: > Correct. > > > On Sunday, May 22, 2016, Anastasia Yendiki > wrote: > >> >> No idea, sorry. You used the -c option with the previous steps of >> trac-all and didn't see this error, correct? >> >&

Re: [Freesurfer] DTI error

Correct. On Sunday, May 22, 2016, Anastasia Yendiki wrote: > > No idea, sorry. You used the -c option with the previous steps of trac-all > and didn't see this error, correct? > > On Sun, 22 May 2016, Jasmin Alves wrote: > > Hi Anastasia, >> Perhaps I was askin

Re: [Freesurfer] DTI error

previous mailing lists, and found no match to this problem. Thank you, Jasmin On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Ok, then you can ignore the error that you see when you run the bedpost > step. > > > `On Sun, 22 May

Re: [Freesurfer] DTI error

Sfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7c1gaW5UpDUs-Df4uqLGaiN1YKi8WpD7PUUFUH_Yh_8&s=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA&e= > What's in the dmri.bedpostX/ directory? > > On Sun, 22 May 2016, Jasmin Alves wrote: > > Output files are being generated, ie. >> 1.

Re: [Freesurfer] DTI error

ki. > > > On Sun, 22 May 2016, Jasmin Alves wrote: > > Hi Anastasia, >> Thank you for the reply, when I do just let it run, I get the following >> error when I try to do trac-all -path –c dmrirc1_sim.txt >> >> I get the following error: >> >> ERR

Re: [Freesurfer] DTI error

< ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Jasmin - Check if things are running despite that error. Are output > files being generated? > > a.y > > On Sat, 21 May 2016, Jasmin Alves wrote: > > >> Dear Freesurfer, >> >> While doin

[Freesurfer] DTI error

Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin Alves Predoctoral Student Medical Biology

[Freesurfer] TRACULA

t; > best, > > Alan > > > > On Tue, Apr 12, 2016 at 11:17 AM, Jasmin Alves > wrote: > >> Hi Alan, >> >> Thank you for your reply. I changed the pathway but now have stumbled >> upon a new error. I tried looking through the feeds and couldn't re

[Freesurfer] TRACULA

nifti format, could this possibly be the cause of this error? I have attached my configuration file for reference. FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 Thanks so much! Jasmin Jasmin Alves Predoctoral

Re: [Freesurfer] error while running dt-recon all

. You can run the following > command and send me the dng.log file > > dt_recon --debug --i DTI.nii.gz --s 40 --o > /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log > > > > > > On 03/16/2016 11:35 AM, Jasmin Alves wrote: > > Do you mean, what en

Re: [Freesurfer] error while running dt-recon all

Do you mean, what ends up happening? I have attached a screen shot of what files are made. On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve wrote: > Can you send me what dt_recon prints to the screen when your run the > command below? > > > On 3/15/16 11:40 PM, Jasmin Alves wro

Re: [Freesurfer] error while running dt-recon all

, 2016 at 12:34 PM, Douglas N Greve wrote: > Can you send the full terminal output from when you run dt_recon with > the nifti as input? > > On 03/15/2016 03:07 PM, Jasmin Alves wrote: > > How was DTI.nii.gz created? DTI.nii.gz was converted from the raw > > dicom data using d

Re: [Freesurfer] error while running dt-recon all

w was DTI.nii.gz created? What happens if you run > mri_info DTI.nii.gz > > If the DICOM is a siemens dicom but has been stripped of special siemens > info, then we cannot unpack it > > > On 03/15/2016 02:02 PM, Jasmin Alves wrote: > > > > Still get the same error: > &g

Re: [Freesurfer] error while running dt-recon all

were directly exported from our siemens scanner > > via Osirix. I also tried running dt_recon using nifti format but that > > resulted in an error as well. Is there anything else I can do? > > > > Thanks, > > > > Jasmin > > > > > > -- > >

[Freesurfer] error while running dt-recon all

occurs, but the files I have were directly exported from our siemens scanner via Osirix. I also tried running dt_recon using nifti format but that resulted in an error as well. Is there anything else I can do? Thanks, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program

[Freesurfer] question about white matter segmentation

white matter, is it necessary to use the voxel edit to remove where the skull is considered part of the white matter mask? Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu

Re: [Freesurfer] abnormal inflated surface

doesn't have the same space as the T1 or white > matter surface, so they are just centered. And overlap one another as > the slice views showed. I'm afraid I can't help with the hippocampal > question, though you may want to try adding some details. > > hth > d > &

Re: [Freesurfer] recon -all errors

st with > > mkdir /Desktop/Brain_Child_subs > > then try rerunning. > Bruce > > > > On Wed, 27 Jan 2016, Jasmin Alves wrote: > > Hi Bruce, >> Could you elaborate on what you mean I need to specify the input volume? >> >> Thanks, >> Jasmin >

Re: [Freesurfer] recon -all errors

UBJECTS_DIR), you still need to specify the > input volume with -i T1_original_joya.nii > > cheers > Bruce > > > On Tue, 26 Jan 2016, Jasmin Alves wrote: > > Bruce, >> Sorry to be a pain, but for some reason, I cannot still get recon-all to >> work. >> >

Re: [Freesurfer] recon -all errors

ll & > > cheers > Bruce > > > On Mon, 25 Jan 2016, Jasmin Alves wrote: > > Hi Bruce, >> Thanks for the reply, I attempted to direct Subjects_dir to the folder >> with >> my data but I received the following error. >> >> Jasmins-MacBook-Pro:Br

Re: [Freesurfer] recon -all errors

is on the command line of recon-all via: > > recon-all -sd ... > > cheers > Bruce > > > > On Sun, 24 Jan 2016, Jasmin Alves wrote: > > Hello Freesurfer, >> >> I am trying to learn freesurfer and ran into the following issues below >> running the rec

[Freesurfer] recon -all errors

.nii -subject joya -a Thank you, Jasmin Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

[Freesurfer] tutorial assistance

he-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh & [2] 5633 Jasmins-MacBook-Pro:glm jasminalves$ ERROR: cannot find /buckner_data/tutorial_subjs/group_analysis_tutorial Thanks! Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program U

[Freesurfer] still receiving permission denied response

ks, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu

Re: [Freesurfer] (no subject)

onvert ? > > On 01/14/2016 05:10 PM, Jasmin Alves wrote: > > > > Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l > > $FREESURFER_HOME/bin/tksurfer > > > > -rwxr-xr-x 1 root wheel 103 May 14 2013 > > /Applications/freesurfer/bin/tksurfer &g

Re: [Freesurfer] (no subject)

links to this mac specific page. > https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall > > ? > > hth > d > > On Thu, Jan 14, 2016 at 5:10 PM, Jasmin Alves wrote: > > Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l > > $FREESURFER_HOME/bin/tksurf

Re: [Freesurfer] (no subject)

Jan 14, 2016 at 2:04 PM, Douglas N Greve wrote: > Jasmin, can you just cut and paste it into the email? > > On 01/14/2016 04:59 PM, Jasmin Alves wrote: > > Here is the output to the ls command > > > > On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves > <mailto:jal..

Re: [Freesurfer] (no subject)

Here is the output to the ls command On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves wrote: > Hi Dr. Greve, > > I am still receiving the same message that I am denied access to freeview. > Is there anything I can do? > > Thanks, > Jasmin > > On Thu, Jan 14, 2016 at 1:22

Re: [Freesurfer] (no subject)

gt; ls -l $FREESURFER_HOME/bin/tksurfer > > > > On 01/14/2016 04:16 PM, Jasmin Alves wrote: > > Hello, > > > > I recently downloaded freesurfer on my mac with a Yosemite operating > > system. The application itself appears to work, however I am not able > > to use th

[Freesurfer] (no subject)

be very useful. Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

[Freesurfer] (no subject)

-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] travel grants for April workshop

Hello, Are there possibly any travel grants available to attend the Freesurfer workshop in April? It would greatly benefit my PhD studies to attend this workshop to learn more about structural techniques, however my PI does not have sufficient funds to send me. Thanks, Jasmin -- Jasmin Alves

[Freesurfer] email

jal...@usc.edu -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer