[Freesurfer] "Upgrade" outputs from 5.3 to 6.0

Is it possible to run Freesurfer 6.0 recon-all -all on a subject previously processed with 5.3 and have 6 utilise the wm, ctrl pt and pial edits (brainmask.finalsurfs.manedit.mgz) made in the 5.3 output? Would it be ok to run -autorecon2-wm -autorecon3 after renaming aseg.mgz to

Re: [Freesurfer] Creating custom aparc.a2009s+aseg.mgz: Shuffled names of parcellations after mris_label2annot

Dear Doug, thank you, adding  --no-unknown indeed fixed the global shuffling of the label names. However, last line of .ctab seems not to be read this time and produced .annot does not contain perirhinal label. My modified .ctab file looks like this:  0  Unknown   0  

[Freesurfer] threshold method used to obtain *exvivo.thresh.labels

Dear experts, Could you please provide me the information how exactly the *_exvivo.thresh.labels have been thresholded? According to this post, http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32542.html .thresh labels are thresholded to pick the most likely vertices that give a

Re: [Freesurfer] multiple expert options files/ wm and control points

Thanks doug. I know the -T flag in mri_fill means  min #of neighbors which must be on to retain a point/specify fill_holes threshold. What does it simply do if I use it in mri_fill‎?  Best, Paul Sent from my BlackBerry 10 smartphone.   Original Message   From: Douglas N Greve Sent: Wednesday,

Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

Was the subject folder that fails ever uploaded? If not please upload and let me know when it's ready and I'll take a look. If it was already uploaded try reuploading as that area get cleared up occasionally. > On Mar 1, 2017, at 5:17 PM, Mira Michelle Raman wrote: > >

Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

HI, I had reported this issue a while ago and have been trying to track it down because it seems to be popping up in strange places on our El Capitan and Sierra machines. So I initially encountered the error dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

Re: [Freesurfer] wm.mgz manual editing

Hi Eli hmm, maybe you should just upload the subject and email us the voxel coords you are talking about? Also, in general it is hard for us to help you unless you include more information. What exact command did you run? What was the screen output? What was in the recon-all.log? cheers

Re: [Freesurfer] Inflated Volume

Hi Anna yes, if you reduce the number of iterations it will inflate less. For example, from the surf dir: mris_inflate -n 1 ./lh.smoothwm ./lh.smoothwm.n1 will generate a slightly inflated surface cheers Bruce On Wed, 1 Mar 2017, Crawford, Anna wrote: > > Hi, > > > I am using a volume

Re: [Freesurfer] WM edit doubt

Hi Manuel have you looked at the aseg? The ventricles are supposed to be filled automatically using it. What FS version are you using? Usually we don't want any surface inside the ventricles (which you have a bit of in your image) cheers Bruce On Wed, 1 Mar 2017, Manuel Delgado wrote: >

Re: [Freesurfer] Question on saving interim files when generating an fsavearge

Hi Douglas. Thanks for the reply. Forgive me for not responding quickly. It turns out what we really want is the interim files that are saved during recon-all if you add the -qcache option. Is there any way to generate those files after running recon-all without having to run recon-all again

[Freesurfer] wm.mgz manual editing

Couple of questions: 1) I edited wm.mgz following the instructions in the wiki guide, but it did not change anything after reconstruction. I am still using 5.3 right now, so maybe the guide is wrong for me. What is the brush value supposed to be? I used 255 but it did not extend the white matter

Re: [Freesurfer] Creating custom aparc.a2009s+aseg.mgz: Shuffled names of parcellations after mris_label2annot

Try adding --no-unknown to the label2annot command line On 02/28/2017 04:45 PM, Antonin Skoch wrote: > Dear experts, > > I would like to create modified aparc.a2009s+aseg file with relevant > parts of parahippocampal cortical ribbon voxel labels replaced by > labels derived from surface labels

Re: [Freesurfer] mri_convert error: \'GetDICOMInfo(): dcmGetDWIParams() 7\' in FS6.0

And this is in version 6? What platform are you using? On 03/01/2017 12:07 PM, Gustav Mårtensson wrote: > > Hi, > > Yes, running mri_convert > ADNI_032_S_0187_MRMPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm > > dummy.mgh still produces the error > > ERROR: GetDICOMInfo():

Re: [Freesurfer] Creating custom aparc.a2009s+aseg.mgz: Shuffled names of parcellations after mris_label2annot

Hi Antonin, I've verified the problem and am working on a solution. doug On 02/28/2017 04:45 PM, Antonin Skoch wrote: > Dear experts, > > I would like to create modified aparc.a2009s+aseg file with relevant > parts of parahippocampal cortical ribbon voxel labels replaced by > labels derived

Re: [Freesurfer] Inflated Volume

Got it! Thank you, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: Wednesday, March 1, 2017 11:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re:

Re: [Freesurfer] Inflated Volume

yea, you have to run it on a surface, usually the white, eg, mris_inflate -n 5 -no-save-sulc lh.white lh.inflated.anna On 03/01/2017 11:45 AM, Crawford, Anna wrote: > I did: > > mris_inflate -n 5 wmparc.mgz inflateTest.mgz > > I wasn't sure oh what my input file should be. It resulted in the

Re: [Freesurfer] Inflated Volume

I did: mris_inflate -n 5 wmparc.mgz inflateTest.mgz I wasn't sure oh what my input file should be. It resulted in the following message: No such file or directory freadFloat: fread failed From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Inflated Volume

what is your mris_inflate command line? On 03/01/2017 11:20 AM, Crawford, Anna wrote: > > Hi, > > > I am using a volume to create a surface overlay. I am currently > overlaying onto the ?h.inflated volumes created when recon-all is > executed. These volumes are overinflated for what I want. Is

Re: [Freesurfer] ERROR: mritotal failed, see transforms/talairach.log

See this web page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview On 03/01/2017 09:48 AM, Hari Guragain wrote: > Hi Freesurfer Community, > > I was trying to run the recon-all for one of the subjects. I got > following error message: > "ERROR: mritotal failed, see

Re: [Freesurfer] multiple expert options files/ wm and control points

Not sure about #3, but the final white surface is created by the second call to mris_make_surfaces. That binary is called twice, the first time it creates the preaparc file On 03/01/2017 09:41 AM, miracle ozzoude wrote: > Thanks Antonin. For 3) what does " min #of neighbors which must be on >

Re: [Freesurfer] Different segmentation atlas

sorry, and what is the gordon parcellation? On 02/28/2017 04:27 PM, Julie Hall wrote: > I'm using the Freesurfer output to register my DWI images to, on which > I would like to apply graph theory on > > > (Sorry I'm a newbie in imaging so let me know if this is not the > answer you're looking

[Freesurfer] Inflated Volume

Hi, I am using a volume to create a surface overlay. I am currently overlaying onto the ?h.inflated volumes created when recon-all is executed. These volumes are overinflated for what I want. Is there a way I can create a less inflated, inflated-volume? I was looking at mris_inflate, and was

Re: [Freesurfer] Manual edit to include missing cortex?

I edited the wm.mgz according to the guide, but it didn't change anything when I ran the reconstruction. What is the brush value supposed to be when editing? 255? On Tue, 2017-02-28 at 08:33 -0500, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to >

Re: [Freesurfer] Total brain volumes

See if this page will answer your questions https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats On 3/1/17 12:39 AM, Daniel Wen wrote: Dear Freesurfer experts, I am new to using freesurfer and was wondering if anyone could explain to me the difference in output generated by

Re: [Freesurfer] mri_vol2surf

Hi Redwan, You'll need to register your volume to an FS-analyzed data set (probably using bbregister). Then apply mri_vol2surf (run with --help to get examples) doug On 2/28/17 5:17 PM, Redwan Maatoug wrote: Hi all ! I would like to convert my files : volumetrics nifti files to surfaces

Re: [Freesurfer] ACPC alignment before or after running on Freesurfer?

Hi Kristine no, it doesn't. Randy Buckner did a small study on this and found no detectable effect cheers Bruce On Tue, 28 Feb 2017, Lee Subin Kristine wrote: > Dear Freesurfer team, > This may sound like a bit of a small question, but I could not find any > exact answer elsewhere. > > Does

Re: [Freesurfer] Building Freesurfer dev with GPU support/CUDA enabled

Hello Francis, Yes, Richard is correct. When doing a local installation you will need the freesurfer data files which do not come with a default clone of the repo. Please see section 1.1 of the build page: $> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page To get

[Freesurfer] ERROR: mritotal failed, see transforms/talairach.log

Hi Freesurfer Community, I was trying to run the recon-all for one of the subjects. I got following error message: "ERROR: mritotal failed, see transforms/talairach.log". The image seems to have some missing hippocampal area. I wonder If we can still run the recon-all? I checked previous archive

Re: [Freesurfer] multiple expert options files/ wm and control points

Thanks Antonin. For 3) what does " min #of neighbors which must be on to retain a point/specify fill_holes threshold" mean exactly? Also, I noticed a difference in FS v5.3 and FS v6.0 ReconAllTable for creating white matter surface. For v5.3, ?h.white is created as one of the outputs for

Re: [Freesurfer] Freeview command line option for multiple screenshots

Hi Peng, You can write all your freeview commands in a text file and call “freeview -cmd cmd.txt”. In cmd.txt, just write commands like this line by line: freeview volume_files -f surface_files … (all the initial file loadings) freeview (other commands such as -cam) -ss screenshot1.jpg

Re: [Freesurfer] Longitudinal hippocampal subfield registered to base

Hi Eugenio, Thanks for your quick response. It would be great to get the probabilistic segmentations for each subfield, it's fine if we have to run the segmentation again. I have only just realised that you now have a longitudinal subfield segmentation pipeline - is this what I'll need to

Re: [Freesurfer] Longitudinal hippocampal subfield registered to base

Dear Amanda The longitudinally processed time points are already in base space. Those transforms you used map base to the original, cross sectionally processed volumes. Regarding individual subfields: you can use mri_extract_label to extract individual labels. You can also obtain probabilistic

[Freesurfer] Longitudinal hippocampal subfield registered to base

Hi All, I have applied the hippocampal subfield segmentation algorithm to each of my time points that have been longitudinally processed. I am now trying to register these back into base space using: mri_convert -T BASE/mri/transforms/TP_to_base.lta -rl BASE/mri/norm.mgz -rt nearest

Re: [Freesurfer] Building Freesurfer dev with GPU support/CUDA enabled

On 1 March 2017 at 03:28, Francis Tyson Thomas wrote: > I have attached the log file as you had requested. This is the error: gzip: testdata.tar.gz: No such file or directory tar: This does not look like a tar archive tar: Exiting with failure status due to

[Freesurfer] Freeview command line option for multiple screenshots

Dear all, I have several different overlays on the same brain surface. When I want to run freeview in command line and take screenshots automatically, I need to restart freeview and load the surface for each screenshot. Is it possible to keep the program on and only change overlays and take

[Freesurfer] (no subject)

Dear all, I am carefully starting up with the basics for analysis of 3T mri images. After having done the recon all I am about to begin the review and editting process where needed. However, I am now a bit overwhelmed. Is there any logical or recommended order to proceed with the several potential

Re: [Freesurfer] Building Freesurfer dev with GPU support/CUDA enabled

Hi Z K, I went ahead and tried your suggestion of running *make install *and these are errors I have, mv ../../distribution/average/?h.EC_average \ /home/tyson/tyson/fs_install/subjects chmod -R 775 /home/tyson/tyson/fs_install/subjects/?h.EC_average rm -Rf

Re: [Freesurfer] Building Freesurfer dev with GPU support/CUDA enabled

Hi Richard, I have attached the log file as you had requested. Thanks, On Tue, Feb 28, 2017 at 3:36 AM, R Edgar wrote: > On 28 February 2017 at 01:10, Francis Tyson Thomas > wrote: > > >