Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

(no subject)
by Ачча Чимагомедова 05 Feb '16

05 Feb '16

Hello! My name is Achcha. I am a PhD student of Russian Medical Academy for Postgraduate Education. In my research "Dementia with Lewy bodies" (DLB) I am going to determine the association between the focal atrophy measures on MRI and to compare it with clinical features of DLB. I try to install FreeSurfer on my computer. But I have only Windows Operating System, that's why I have got and installed VirtualBox. Could you please send me detailed instructions and help to install FreeSurfer. Thank you, Kindest regards Achcha Chimagomedova

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Error on Linux
by Ankita Chatterjee 30 Jan '16

30 Jan '16

Hello, I am trying to run freesurfer on a machine I got access to that has Ubuntu (14.04) on it. When I run the tutorials and try to run qdec or freeview, I get this error - qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory I tried running sudo ln -s libjpeg.so.8 libjpeg.so.62, but it says libjpeg.so.62 already exists. Any ideas? I ran tkmedit and tksurfer and those run fine - only freeview and qdec are giving this error. Thanks! Ankita

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Re: [Freesurfer] fast_selxavg3 error when Octave is used
by Douglas N Greve 30 Jan '16

30 Jan '16

Does octave now have a version of textread? I looked over my notes and saw that it did not support it at one point, which I apparently forgot and put it into the code. Can't do much about your space issue On 01/29/2016 11:37 AM, m.abouelyazid(a)gmail.com wrote: > > Okaii, so I fixed that last issue by changing the version of octave > installed then I found I needed to install FSL also. Problem is… now > the virtual machine drive has run out of space… > > Sent from Mail <http://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > *From: *m.abouelyazid(a)gmail.com <mailto:m.abouelyazid@gmail.com> > *Sent: *Friday, January 29, 2016 12:01 PM > *To: *Douglas Greve <mailto:greve@nmr.mgh.harvard.edu> > *Subject: *RE: [Freesurfer] fast_selxavg3 error when Octave is used > > Are there any other paths that I need to add? because now I get > another error > > Extension format = nii.gz > > error: `textread' undefined near line 210 column 17 > > error: evaluating argument list element number 1 > > error: evaluating argument list element number 1 > > error: called from: > > error: /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m at line > 210, column 10 > > error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line > 53, column 9 > > > *From: *Douglas Greve <mailto:greve@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 11:41 AM > *To: *m.abouelyazid(a)gmail.com <mailto:m.abouelyazid@gmail.com>; free > surfer <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used > > yes > > On 1/28/16 9:31 PM, m.abouelyazid(a)gmail.com > <mailto:m.abouelyazid@gmail.com> wrote: > > I am running on the virtual machine where I don’t have MATLAB so I > installed Octave… > > Maybe I should include the folder into the Octave path? > > > *From: *Douglas Greve <mailto:greve@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 11:27 AM > *To: *m.abouelyazid(a)gmail.com <mailto:m.abouelyazid@gmail.com>; > freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used > > Is that directory in your matlab path? does it run properly in matlab? > > On 1/28/16 8:36 PM, m.abouelyazid(a)gmail.com > <mailto:m.abouelyazid@gmail.com> wrote: > > Yes, it exists in the location you mentioned… > > > *From: *Douglas N Greve <mailto:greve@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 2:27 AM > *To: *freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is > used > > Does fast_fileexists.m exist in $FREESURFER_HOME/fsfast/toolbox ? > > On 01/28/2016 07:16 AM, m.abouelyazid(a)gmail.com > <mailto:m.abouelyazid@gmail.com> wrote: > > > > > > Since I am a windows user I got the Virtualbox version of > FreeSurfer > > > and to use fs fast, I installed Octave on the virtual > machine, I set > > > the environment variables and then when I run the command > > > > > > selxavg3-sess -analysis rtopy.lh -sf sessid > > > > > > which runs a retinotopy analysis, I get the following error: > > > > > > sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx > > > > > > sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess > -analysis > > > rtopy.lh -sf sessid > > > > > > error: `fast_fileexists' undefined near line 5 column 4 > > > > > > ------------------------------------------ > > > > > > ERROR: fast_selxavg3() failed\n > > > > > > Any idea of the cause of this error and how to run around? > > > > > > Thank you, > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto: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 whom it is > > addressed. If you believe this e-mail was sent to you in error > and the e-mail > > contains patient information, please contact the Partners > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > > but does not contain patient information, please contact the > sender and properly > > dispose of the e-mail. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] tracula quality assessment dwi_motion.txt units
by Ruth Carper 29 Jan '16

29 Jan '16

Anastasia, Thanks for the quick reply.And millimeters for the translation? Ruth

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Wm correction
by maryam koochaki 29 Jan '16

29 Jan '16

Hi Bruce, I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral Ventricle. As you can see in the image attached, the big part is excluded in both hemisphere. I tried to fill it by editing wm volume but the problem still exists.Do you have any suggestion?Thanks,Maryam

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HSF in 5.3
by Alan Francis 29 Jan '16

29 Jan '16

Hi Eugenio: I am trying to run the HSF method on 42 subjects. The FS version on our cluster is 5.3. However when I use the following command I get an error message. [alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields ERROR: Flag -hippocampal-subfields unrecognized. -s Smoke_d004 -hippocampal-subfields Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I tried adding the -hippocampal-subfields-T1 but that did not work too. thanks, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh
by Erik Lindberg 29 Jan '16

29 Jan '16

Dear Bruce and Freesurfer, Yes, that is what I am saying! This what appears in the commandprompt when running the command: input cache.th13.abs.sig.cluster.mgh frame 0 nErode3d 0 nErode2d 0 output thresholded.mgh Binarizing based on threshold min 1.3 max +infinity binval 1 binvalnot 0 Found 12485 values in range Counting number of voxels Found 12485 voxels in final mask mri_binarize done Yet nothing is visible when I open the thresholded surface in tksurfer. previous: what was the command line and screen output of the binarization? And are you saying that pre-binarization you have locations that are above threshold, but they are set to 0 anyway?

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mri_convert and image orientation
by Yang, Daniel 29 Jan '16

29 Jan '16

Dear FreeSurfer experts, I find that mri_convert will convert DICOM of structural scan to neurological orientation by default. For example, mri_convert --in_type dicom --out_type mii <first file in the DICOM directory> <output.nii.gz> Thus, the NII may need to be swapped in x for use in FSL. In this the case? Many thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang(a)yale.edu

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Re: [Freesurfer] fast_selxavg3 error when Octave is used
by Douglas Greve 28 Jan '16

28 Jan '16

yes On 1/28/16 9:31 PM, m.abouelyazid(a)gmail.com wrote: > > I am running on the virtual machine where I don’t have MATLAB so I > installed Octave… > > Maybe I should include the folder into the Octave path? > > > *From: *Douglas Greve <mailto:greve@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 11:27 AM > *To: *m.abouelyazid(a)gmail.com <mailto:m.abouelyazid@gmail.com>; > freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used > > Is that directory in your matlab path? does it run properly in matlab? > > On 1/28/16 8:36 PM, m.abouelyazid(a)gmail.com > <mailto:m.abouelyazid@gmail.com> wrote: > > Yes, it exists in the location you mentioned… > > > *From: *Douglas N Greve <mailto:greve@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 2:27 AM > *To: *freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used > > Does fast_fileexists.m exist in $FREESURFER_HOME/fsfast/toolbox ? > > On 01/28/2016 07:16 AM, m.abouelyazid(a)gmail.com > <mailto:m.abouelyazid@gmail.com> wrote: > > > > > > Since I am a windows user I got the Virtualbox version of > FreeSurfer > > > and to use fs fast, I installed Octave on the virtual machine, I > set > > > the environment variables and then when I run the command > > > > > > selxavg3-sess -analysis rtopy.lh -sf sessid > > > > > > which runs a retinotopy analysis, I get the following error: > > > > > > sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx > > > > > > sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -analysis > > > rtopy.lh -sf sessid > > > > > > error: `fast_fileexists' undefined near line 5 column 4 > > > > > > ------------------------------------------ > > > > > > ERROR: fast_selxavg3() failed\n > > > > > > Any idea of the cause of this error and how to run around? > > > > > > Thank you, > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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 > whom it is > > addressed. If you believe this e-mail was sent to you in error and > the e-mail > > contains patient information, please contact the Partners > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > > but does not contain patient information, please contact the > sender and properly > > dispose of the e-mail. >

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fast_selxavg3 error when Octave is used
by m.abouelyazid＠gmail.com 28 Jan '16

28 Jan '16

Since I am a windows user I got the Virtualbox version of FreeSurfer and to use fs fast, I installed Octave on the virtual machine, I set the environment variables and then when I run the command selxavg3-sess -analysis rtopy.lh -sf sessid which runs a retinotopy analysis, I get the following error: sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -analysis rtopy.lh -sf sessid error: `fast_fileexists' undefined near line 5 column 4 ------------------------------------------ ERROR: fast_selxavg3() failed\n Any idea of the cause of this error and how to run around? Thank you,

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Freesurfer January 2016