Re: [Freesurfer] Infant freesurfer

  _ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lilla Zollei Sent: Wednesday, April 22, 2020 3:02 PM To: Freesurfer support list Subject: Re: [Freesurfer] Infant freesurfer   Yes, I would

Re: [Freesurfer] Infant freesurfer

?  _ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lilla Zollei Sent: Wednesday, April 22, 2020 2:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] Infant freesurfer   Hi Colleen, The manual editing option has not yet been

Re: [Freesurfer] Infant freesurfer

Hi Colleen, The manual editing option has not yet been added to the pipeline. Best, Lilla On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote: > > Hello. I am working with the infant Freesurfer pipeline. I have noticed that > some of our subjects may need to be manually edited, and then run through

Re: [Freesurfer] (no subject)

Our default setting to run mrri_cvs_register on our cluster is to use 35gb. Lilla On Tue, 29 Oct 2019, Nader Razmara wrote: Hi expertsI use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram. When i use mri_cvs_register as: mri_cvs_register --mov subjid --mni or  mri_cvs_register --mov subjid

Re: [Freesurfer] [mri_cvs_register] Transform is zero

Hi Stefano, If you suspect that the error is due to the small deformation values, can you try to use -odt float to specify the output data format? Lilla On Tue, 29 Oct 2019, Stefano Zappala wrote: Hi there, I am having problem reading the final_CVSmorph_toS131032017_Supine.m3z

Re: [Freesurfer] Thalamic subnuclei color table

Hi Anna, See attached. Lilla On Fri, 25 Oct 2019, Crawford, Anna wrote: External Email - Use Caution Hello, Just a quick question. We recently installed the new thalamus segmentation subroutine.  It’s really wonderful, and much promise to our work. I can’t find a

[Freesurfer] segmentation tablet

Hi All, We are looking into replacing our old Wacom segmentation tablet and the two options that I have found so far are the * Wacom Cintiq Pro 32 and * Microsoft Surface Studio 2 Neither of these are linux compatible, which has created some issues in the past. Are there any groups out

Re: [Freesurfer] FS6.0 on 2yo subjects

Hi Dimitrios, Agree with Burce. The youngest we have processed with the standard pipeline was about 4.5yrs. Lilla On Wed, 18 Sep 2019, Bruce Fischl wrote: Hi Dimitrios it's kind of an empirical question. Lilla does have some newer tools you might consider instead of things aren't as

Re: [Freesurfer] Using Freesurfer Commands for Neonate

"mri_aparc2aseg" should work. Lilla On Fri, 2 Aug 2019, Mahshid Fouladivanda wrote: Dear Experts,   I have a neonate  MRI Image which its parcellation file, surface files and the ribbon are not created by freesurfer. I have created an annotation file for it using "write_annotation". Now,

Re: [Freesurfer] input image for infantFS

s registration flag and not an infant_recon one. Best, Lilla > > On Thu, Jul 11, 2019 at 3:26 PM Lilla Zollei > wrote: > > Hi Mahmoud > > Currently the -i flag is not activated. I can add that in a bit. > > Can you create soft links to your inpu

Re: [Freesurfer] input image for infantFS

Hi Mahmoud Currently the -i flag is not activated. I can add that in a bit. Can you create soft links to your input images? Lilla On Thu, 11 Jul 2019, Mahmoud wrote: > > Hi all, > I have my data organized in this way: > study/sub/T1/data.nii.gz > > infantFS wants the input as

Re: [Freesurfer] 1.5T Infant Brain Analysis

Hi Anna, We have not tried the pipeline on 1.5T data, but you are welcome to download the beta version and see how well it is doing. https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS Lilla On Thu, 11 Apr 2019, Crawford, Anna wrote: > > Hello, > > > I was looking to use the Freesurfer

Re: [Freesurfer] applyMorph gives (10000 10000 10000) coordinates

__ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lilla Zollei Sent: Thursday, February 7, 2019 10:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] applyMorph gives (1 1 1) coordinates   Hi Noam, Maybe a I am a bit confused

Re: [Freesurfer] applyMorph gives (10000 10000 10000) coordinates

Hi Noam, Maybe a I am a bit confused but in the attached file I do not see the (1 1 1) coordinate that correspond to invalid coordinate locations. Is the file that you attached your electrodes_morph_to_colin27.txt or is it the terminal output? Lilla On Thu, 7 Feb 2019, Peled,

Re: [Freesurfer] SUIT FS-FAST

We are currently working on including cerebellar parcellation in the FS recon pipeline, but this feature is not yet available. Independently, you could import and use the SUIT ROIs, but we do not have a pipeline for that. On Thu, 15 Nov 2018, std...@virgilio.it wrote: Is available the

Re: [Freesurfer] mri_cvs_register using fsaverage

__ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lilla Zollei Sent: Wednesday, August 1, 2018 2:33:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

Re: [Freesurfer] Surface Area in Toddlers/Children

Hi Derek, We do not use the standard FS pipeline for the analysis of the age group of your interest. In general, we have seen it being successfully used on subjects down to 4.5yrs of age, but 25 mo is quite young to be analyzed by the adult template. I assume, without seeing your data, that

Re: [Freesurfer] mri_cvs_register using fsaverage

__ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lilla Zollei Sent: Wednesday, August 1, 2018 8:35:49

Re: [Freesurfer] mri_cvs_register using fsaverage

Hi Noam, Can you can use the --mni flag? "Use the CVS atlas in MNI152 space as a target for registration (as opposed to the default CVS template)" Lilla On Wed, 1 Aug 2018, Peled, Noam wrote: I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't

Re: [Freesurfer] Infant atlas/pipeline

Hi Kelli, Our beta version is ready and I can set you up with it. Please, send me a note directly and I can help you with that. Lilla On Sun, 8 Jul 2018, Dominick, Kelli wrote: External Email - Use Caution Hello Freesurfer Experts,  I am hoping to use Freesurfer in

[Freesurfer] about Rahul Desikan

Hi All, Many of you might know Rahul personally from his time spent in Boston, at the Martinos Center and on Freesurfer (eg.: 'Desikan-Killiany' cortical atlas). The below is a great piece about his current struggles with ALS (and amazing work productivity):

Re: [Freesurfer] no skullstrip

Hi Aicha. We have a different processing stream for infants. It is not only the skullstripping that will not work for your cases but much of the remaining pipeline. We are getting ready to release that pipeline. Lilla On Fri, 12 Jan 2018, Dijkshoorn, A.B.C. (Aicha) wrote: Dear free

Re: [Freesurfer] Nonlinear CVS registration into average brain rdinates

Hi David and Noam, I have fixed a bug in applyMorph. If you have access to the dev version of the code base that should be available to you in a day. If not, send and email to the list and we can provide you with it. Here are the steps: (1) Run mri_cvs_register command. As the applyMorph

Re: [Freesurfer] Does this analysis work for new born baby

The currently available FS pipeline does not work for newborn infant brain MRI. Lilla On Tue, 2 Jan 2018, Ting Li wrote: > Dear Stuff, > > Happy new year. > > Does Freesurfer work for new born baby MRI or not? If I want to use it for > baby MRI, what should I pay attention to? Thanks a lot! >

Re: [Freesurfer] free surfer v5 & 6

Hi Gianluca, > I am working with data coming from two different versions of Freesurfer, v5.1 > and v6. > As measurements looks different (an excerpt below from aseg.stats files), I > am trying to see if that difference is statistically relevant. > Could you anticipate something with this

Re: [Freesurfer] neonatal brain

pared to or just as a common spatial coordinate space where you can do your comparison? Best, Lilla > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei > [lzol...@nmr.mgh.harva

Re: [Freesurfer] neonatal brain

Hi Aicha, We do have a pipeline and I am trying to get it released by the end of the year. You should be able to build your own template independent from the adults, but you will not be able to just plug this new one in to the adult processing pipeline. Lilla On Mon, 27 Nov 2017,

Re: [Freesurfer] QC on CVS registration

Hi Chintan, Can you send your snapshot again? I do not have access to the attachment. Best, Lilla On Mon, 13 Nov 2017, Mehta, Chintan wrote: Dear FreeSurfer users, I'm using FS 6.0. I registered MRI scans to the CVS-Avg35 template (mri_cvs_register) and viewed output. While the nonlinear

Re: [Freesurfer] Newborn MRI segmentation

The neonatal pipeline and its atlasesis not yet released. I am working on it, so hopefully you do not need to wait long. Lilla On Thu, 21 Sep 2017, Paula Diniz wrote: > Hi experts! > > I want to perform recon-all pipeline on newborn MRI data. > > How I can do this? Which atlas you

[Freesurfer] postdoc ad

Please, see attached or below for details. Lilla Postdoctoral Research Fellow Position in Infant Brain MRI analysis at the A.A. Martinos Center, MGH and Harvard Medical School under Dr. Lilla Zöllei A postdoctoral fellow is recruited for an NIH funded project for developing

[Freesurfer] Fwd: Microstructure imaging - finding a postdoc (fwd)

-- Forwarded message -- De: Cyril Poupon Dear All, please transfer this post-doc proposal to your post-docs or PhD students who could be interested to apply for a post-doc in Tim Dyrby's lab in Denmark to develop methods to probe brain tissue

Re: [Freesurfer] Freesurfer pipeline for infant

Hi Gianluca, For your younger ages, this is the wiki that I would check: https://surfer.nmr.mgh.harvard.edu/fswiki/ChildBrainManualEdits We will look into the stats file. Best, Lilla On Tue, 11 Jul 2017, Gianluca Sforza wrote: Hi Lilla,is there a range of age I should possibly take more

Re: [Freesurfer] Pediatric Atlas/Template

Hi Jess, Yes, there are. But currently we are focusing on the 0-2yrs age range. Your age range of interest will come after that. Lilla On Thu, 13 Jul 2017, Jessica Reynolds wrote: I am wondering whether there are still plans to implement a pediatric atlas/template? I’m working with

Re: [Freesurfer] recon-all on newborn

easy for me to understand the gap. > many thanks > Sarbani > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei > [lzol...@nmr.mgh.harvard.edu] > Sent: 05 July 2017 22:32 > T

Re: [Freesurfer] recon-all on newborn

rcellation Statistics >Cortical Ribbon Mask >Cortical Parcellation mapping to Aseg > > BW > S Das > ________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei > [lzol...@nmr.mgh.harvard.edu] > Sent: 04 Ju

Re: [Freesurfer] recon-all on newborn

Hi S Das, We are trying to release the infant pipeline by the end of the summer. Lilla On Tue, 4 Jul 2017, Das S. wrote: > Dear Freesurfer expert, > I want to perform recon-all pipeline on neonates data.Can I do so? > I was going through some mail archives and there it is said that on T1

Re: [Freesurfer] Freesurfer parcelations of cortical regions in TrackVis

Hi Cris, As long as your parcellation file gets resampled into the diffusion space, you should not have any trouble reading it into TrackVis. When defining ROIs you can just select individual label values afterwards. Lilla On Thu, 15 Jun 2017, Leyton Moscoso, Cristian Eduardo wrote: Hi

Re: [Freesurfer] Haskins Pediatric Atlas use in FS

Hi Jack, We do not have such an automated option at the moment. Lilla On Thu, 25 May 2017, John Hettema wrote: To FreeSurfer team,   I have child MRI data for which it would be best to use a pediatric atlas/template for warping, alignment, and labeling. I am aware of the Haskins

Re: [Freesurfer] apply CVS morph to a list of coordinates

Hi Cristian, Can you send me the original mri_cvs_register command? When I apply the m3z transform to your moving volume the result is not registered to the target. set morph = combined_toColin27_elreg_aseg.m3z set targ = N27orig.mgz set mov = TS076CDorig.mgz set out = ${mov:r}.2.${targ}

Re: [Freesurfer] apply CVS morph to a list of coordinates

Hi Cristian, Can you upload your files for us? https://gate.nmr.mgh.harvard.edu/filedrop2/ Lilla On Tue, 28 Feb 2017, Donos, Cristian wrote: Hi, I was able to apply the morph using combined_toColin27_elreg_aseg.tm3d instead of fullCSVmorph.tm3d. The resulting coordinates are wrong, but it

Re: [Freesurfer] mri_cvs_register error : PETSC Error

[linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png] On Mon, Feb 20, 2017 at 4:43 PM, Lilla Zollei <lzol...@nmr.mgh.harvard.edu> wrote: Hi Bhavana, We recommend to assign about 35GB of RAM on our cluster nodes for this operation. I am not sure how that co

Re: [Freesurfer] Output from mri_cvs_register

That is the same. You shoudl be fine. Lilla On Mon, 20 Feb 2017, Magnús Ingvi wrote: Hi!I am running mri_cvs_regsiter, on the cvs_avg35 space. In the dt_recon tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion ), the expected .m3z output file is called

Re: [Freesurfer] apply CVS morph to a list of coordinates

Hi Cristian, The below error message indicates that your morph cannot be read. How much memeory do you have on the machine where you are running this operation? Lilla On Fri, 10 Feb 2017, Donos, Cristian wrote: Hi, I have registered a patient’s MRI over the ColinN27 with mri_cvs_register

Re: [Freesurfer] 答复: Longitudinal proceesing for Pediatric data

Hi Dong, What is the age range that you are working with? Lilla On Mon, 20 Feb 2017, Martin Reuter wrote: No, not that I know of. Also I expect that it also depends on other factors (like image resolution, quality, subject anatomy etc) . Best, Martin Am 15.02.2017 um 08:21 schrieb

Re: [Freesurfer] mri_cvs_register error : PETSC Error

to the function. Regards, Bhavana [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png] On Mon, Feb 20, 2017 at 12:21 PM, Lilla Zollei <lzol...@nmr.mgh.harvard.edu> wrote: Hi Bhavana, How much memory are you allocating to this process?

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Hi Bhavana, How much memory are you allocating to this process? Lilla On Mon, 20 Feb 2017, Bhavana Ganesh wrote: > Hi Developers, > > I'm receiving this error while I try to run mri_cvs_register. The same error > was received when I reran the same even after increasing the memory allocated

Re: [Freesurfer] mri_cvs_register: how to read/import .m3z warp file

Hi Stefano, You can try to use the attached matlab file for reading the m3z file. Lilla On Mon, 30 Jan 2017, Stefano Zappalà wrote: Dear FreeSurfer Developers, I am trying to visualize and modify the output warp field (in .m3z) of a mri_cv_registration call aimed at aligning a T1w scan

Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

look OK? I tried these commands, but the results were not great so I suspect that something is incorrect in the syntax and/or inputs. Thanks for your help! Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: douglas_merki...@rush.edu On Jan 26, 2017, at 8:42 AM, Li

Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs

Hi Doug, In order to compute and apply the inverse of an m3z transform you would need to use the --inv-morph flag instead of the --m3z and reverse your targ and mov inputs. With the current implementation of mri_vol2vol though I do not think that you can specify the order of the transforms

Re: [Freesurfer] createMorph & applyMorph: unexpected results

Hi Stefano, If you have the final_CVSmorph_toSynthF.m3z file you can use mri_vol2vol dirctly to apply it to another volume. Look for examples in mri_cvs_register --help. We are moving away from using the tm3d file format. Lilla On Wed, 11 Jan 2017, Stefano Zappalà wrote: Hello

Re: [Freesurfer] mri_cvs_register

Hi Nazanin, You need to run the full recon on your subject before you can use this registration command. Lilla On Sat, 24 Dec 2016, N Saf wrote: Dear Freesurfers, I try to register my subject with cvs atlas in mni space I use this command mri_cvs_register --mov subject.nii --mni I got

Re: [Freesurfer] Infant brain atlas

The manually segmented brains exist. They will not be part of FS 6.0, but we are planning an independent release for them early next year. Lilla On Thu, 15 Dec 2016, Axelson, Eric D wrote: I asked this last week with no response:   Does the infant brain atlas mentioned in this paper

Re: [Freesurfer] Registration

Hi Bob, We are moving towards only using m3z files and the only reason you still see tm3d files in your output is that you are using the --nocleanup flag so all intermediate results are kept in your output directory. So this means that you will not need to use the applyMorph tool. The two

Re: [Freesurfer] Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall

Hi Gajendra, The recon stream exists in a beta version and will not make it to 6.0. I am hoping to release the stream and the atlas though before the end of the year. Lilla On Thu, 29 Sep 2016, GAJENDRA KATUWAL (RIT Student) wrote: Hello FreeSurfer experts, I am considering using

Re: [Freesurfer] CVS question

Hi Michael, I want to compare two populations using CVS so I can cross-register multimodal maps (e.g. ASL, FA, QSM) for volumetric comparisons. I’ve gotten CVS to work very well registering one subject to another, it really is impressive However, using the --mni option, it doesn’t work so

Re: [Freesurfer] Using digital tablet pen

Hi Mahmoud, At the below link you will find some suggestions / settings that we use with our Cintiq tablet: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewSegmentations "Segmenting using a Cintiq tablet or display" Best, Lilla On Tue, 22 Mar 2016,

Re: [Freesurfer] mri_cvs_register : output

Hi Elijah, Yes, it is. Lilla On Sun, 20 Mar 2016, Elijah Mak wrote: Hi Freesurfer Community, I am running mri_cvs_register for the spatial normalization and it seems to work very nicely on my set of DTI data in subjects with substantial atrophy.  However, I can't seem to find the file 

[Freesurfer] 12th International Summer School on Biomedical Imaging, Abbaye de Saint Jacut, Brittany, France, June 16-24, 2016. (fwd)

FYI: this is a great program for PhD students and postdocs. -- Forwarded message -- Date: Wed, 20 Jan 2016 17:09:55 +0100 From: Christian ROUX To: ROUX Christian Subject: 12th International Summer School on Biomedical Imaging,

Re: [Freesurfer] register image to mni152

Hi John, In order to use bbregister you would first need to recon your data set as the registration algorithm relies on surfaces. After that Usage: bbregister --s --mov --reg -- Help: bbregister --help Lilla On Sun, 17 Jan 2016, John Anderson wrote:   Dear experts, I wanted to

Re: [Freesurfer] bring volumes to fsaverage space

Hi Shani, Sure. You can do mri_cvs_register --help and that should give you lots of information. Alternatively you can also go to https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register and read through the presentation that we give at the FS course:

Re: [Freesurfer] Issue with converting aseg.mgz file to .nii file

Hi Jon, What is the exact command that you used for the below described conversion? Lilla On Fri, 31 Jul 2015, Jonathan Plasencia wrote: I've converted the aseg.mgz file to .nii (need data in nii to do some further work on the data). However, the number of voxels for a given structure

Re: [Freesurfer] Issue with converting aseg.mgz file to .nii file

On Fri, Jul 31, 2015 at 12:31 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote:        Hi Jon,        What is the exact command that you used for the below described        conversion?        Lilla        On Fri, 31 Jul

Re: [Freesurfer] Freesurfer tool for children's data

: Mittwoch, 24. Juni 2015 16:37 An: Freesurfer support list Betreff: Re: [Freesurfer] Freesurfer tool for children's data Hi Kristina what age? It works reasonably well down to 7 or even 5. Younger than that is something that Lilla Zollei has made a lot of progress on, but isn't ready

Re: [Freesurfer] mri_cvs_register using high resolution images

Oh, I see you do not have a recon for your high res volume. Could you try the below mri_vol2vol command with an additional -lta flag that has the transform that you computed to align your lowres and high res volumes? Lilla On Wed, 6 May 2015, Celine Louapre wrote: Thank you Lilla for the

Re: [Freesurfer] Convert between .m3z and .tm3d format outputs from mri_cvs_register

You can use createMorph: createMorph --out $tm3d --template $template \ --subject $moving --in gcam $m3z --Lilla On Wed, 25 Feb 2015, Zachary Greenberg wrote: I using mri_cvs_register and applyMorph on a linux server ( freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) and I

Re: [Freesurfer] topology defect in freesurfer

Hi Shaheen, Freesurfer does not handle that age-range so it is not applicable for neonates. Send me an email and I will tell you what we are developing now that might be appropriate for you. Lilla On Fri, 6 Feb 2015, Shaheen Ahmed wrote: Hello,  I am using freesurfer for neonates but

Re: [Freesurfer] recon-all dimensions

Hi Jeff, Yes that is the very first step in the recon-all processing. Lilla On Thu, 5 Feb 2015, jwa...@nmr.mgh.harvard.edu wrote: Hello Freesurfer, My MPRAGE dimensions are 1x1x1.33. The output of recon-all appears to be 1x1x1, judging by the fact that the aseg.stats columns for voxel

Re: [Freesurfer] applyMorph to 3d voxel coordinate list

Hi Zach, You would call it like the following: applyMorph --template $t --transform $m point_list $i $o linear wheer t is the template volume, m is the tm3d morph file, i is the input o is the output and linear refers to the type of interepolation. Lilla On Wed, 4 Feb 2015, Zachary Greenberg

Re: [Freesurfer] Infant MRI segmentation

Hi Berdakh, We do not have any publicly available processing stream that would work for this age range. I do have some preliminary tools though, so if you are interested send me an email with a bit more details about your dataset and I can tell you whether I could help. Lilla On Tue, 27 Jan

Re: [Freesurfer] Fwd: Eccentric lesions (fwd)

Hi Octavian, If you have an OK aseg volume, you could try to fit a surface over it using mris_make_surfaces with the -cover_seg flag. Lilla On Tue, 25 Nov 2014, Bruce Fischl wrote: -- Forwarded message -- Date: Tue, 25 Nov 2014 08:05:55 -0600 From: Octavian Lie

Re: [Freesurfer] Fwd: Fwd: Eccentric lesions

Hi, Could you use a colormap for your aseg? It is really hard to see the different ROIs on a grayscale image. Thanks, Lilla On Wed, 26 Nov 2014, Octavian Lie wrote: Dear Lilla, Here is a snapshot of the aseg volume, which rescues some gray matter not included in the pia. I am not sure if

Re: [Freesurfer] FreeSurfer GUI tutorial

Hi Piotr, There are several tutorials that describe our standard data processing pipeline. You can start by looking at: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial with Introduction to Freesurfer and Analyzing the Individual Subject. If you have any further questions, please, send

Re: [Freesurfer] Out of memory error on mri_cvs_register

file you can find the log of this command. Best regards, Mohammadi-Nejad On Monday, September 29, 2014 2:12 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Mohammadi-Nejad, Could you include the command that you submitted and the error message and log file from when the process

Re: [Freesurfer] Out of memory error on mri_cvs_register

Hi Mohammadi-Nejad, Could you include the command that you submitted and the error message and log file from when the process terminated? Lilla On Mon, 29 Sep 2014, Ali-Reza Mohammadi-Nejad wrote: Hi I am trying to do an mri_cvs_register for two subjects analyzed with FS-5.1.0 on a

Re: [Freesurfer] mri_cvs_register

Hi Ben, What version of freesurfer are you using? Lilla On Wed, 10 Sep 2014, bigben2...@web.de wrote: Hey everyone,   i have tried to run the mri_cvs_register command but it returned an error in the second step. It returned:   VolumeMorph load - failed to open input stream   I have

Re: [Freesurfer] mri_cvs_register

Could you also send the log file along? Thanks, Lilla On Wed, 10 Sep 2014, bigben2...@web.de wrote: I'm using the version stable v5.3.0. Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Fwd: Jacobian mri_cvs_register

]  reg_IBSR_01_2_IBSR_02_brain.nii.gz ​​[icon_10_generic_list.png]  jacobian.nii.gz ​Regards, Andre Santos Ribeiro PhD Student, Imperial College London On Tue, Aug 5, 2014 at 4:24 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Andre, What do you mean by they do not seem to match voxel-wise

Re: [Freesurfer] Fwd: Jacobian mri_cvs_register

the applyMorph, and subtract the initial virtual 4d image. The Jacobian matrix can also be calculated through this fields. That is definitely one way of doing it. Best, Lilla On Wed, Aug 6, 2014 at 3:35 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Andre, The jacobian field

Re: [Freesurfer] Jacobian mri_cvs_register

for this question in advance. Regards, Andre Santos Ribeiro PhD Student, Imperial College London On Fri, Jul 11, 2014 at 4:11 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi, First, in the mri_cvs_register I kept all the files and therefore

[Freesurfer] RA position available in Neuroimaging of Multiple Sclerosis

Contact Caterina Mainero, M.D. (cater...@nmr.mgh.harvard.edu) if interested! A full-time Research Technologist (Assistant) position is available in the field of Neuroimaging of Multiple Sclerosis (MS) at the A. A. Martinos Center for Biomedical Imaging of Massachusetts General Hospital (MGH).

Re: [Freesurfer] uploading a surface in freeview

Hi Carina, You can use the -f option (instead of -v used for volumes) when you are calling freeview from the commandline in order to display a surface and then append :overlay=overlay_filename after the filename to identify the overlay that you want to use. You will need to decide which hemi

Re: [Freesurfer] Jacobian mri_cvs_register

AM, André Ribeiro af...@imperial.ac.uk wrote: Thank you! Didn't realized that function existed. Regards, Andre Santos Ribeiro On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Andre You can run: mri_jacobian -tm3d 3d morph

Re: [Freesurfer] Jacobian mri_cvs_register

, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi, You should use the final m3z file. The -tm3d flag just indicates that the file was created by mri_cvs_register. Lilla On Fri, 11 Jul 2014, André Ribeiro wrote: I got an error using the mri_jacobina

Re: [Freesurfer] Jacobian mri_cvs_register

Hi Andre You can run: mri_jacobian -tm3d 3d morph template volume output volume --Lilla On Thu, 10 Jul 2014, André Ribeiro wrote: Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis?

Re: [Freesurfer] DTI FA Values in Diffusion Space vs. Standard Space

Hi Emily, You will need to resample them in a common space before you do group analysis. Lilla On Tue, 1 Jul 2014, ebell...@uwm.edu wrote: Hello, I was wondering if it is better to keep the FA results from a DTI analysis in diffusion space for group analysis or if you should warp them

Re: [Freesurfer] Recon All on a 3 years old subject

Hi Francesco, The FS recon stream is set up for adult image analysis. In the past we have had success with analysing data sets of children, but below the age of 4yrs the success rate really drops and the stream is not recommended. We are working on a separate stream for that population, but

Re: [Freesurfer] reconstruction problem with pediatric images

are in the process of creatig a pipeline for them, but it is not yet ready for distribution. Lilla On Thu, 20 Mar 2014, Francesco Baldacchini wrote: Hi Lilla, They range from neonates to 6 years old, Francesco 2014-03-19 19:21 GMT+01:00 Lilla Zollei lzol...@nmr.mgh.harvard.edu: Hi

Re: [Freesurfer] reconstruction problem with pediatric images

Hi Francesco, How old are your subjects? Lilla On Wed, 19 Mar 2014, Francesco Baldacchini wrote: I have some quality problems with my scans. I'm trying to run recon-all on pediatric brain images but, given the low contrast between cortical regions and the white matter, I do consistently

Re: [Freesurfer] setting the useRealRAS bit

Doug, mris_convert does not read / write that information either. On Sun, 9 Feb 2014, Bruce Fischl wrote: really? I didn't realize that as I don't use them much. Doug: do you have something like MRISread? On Sun, 9 Feb 2014, Lilla Zollei wrote: Those .m files only give me a set

[Freesurfer] setting the useRealRAS bit

Hi, I have some FS-style surface files that were created using outside tools (from McGill). Due to some recent changes in FreeView they do not display properly though as the useRealRAS bit in the header is not set to 1. Do we have any C / Matlab code that I could use to change that? Thanks,

Re: [Freesurfer] setting the useRealRAS bit

guess you will need to figure out how to get the right ras2vox matrix into them cheers Bruce On Sun, 9 Feb 2014, Lilla Zollei wrote: Hi, I have some FS-style surface files that were created using outside tools (from McGill). Due to some recent changes in FreeView they do not display

Re: [Freesurfer] Destrieux Atlas with Kid brains

step. Lilla On Tue, 28 Jan 2014, Lilla Zollei wrote: I would say that for 5-8 the atlas would probably work. Below 5 I would be skeptical. There is no alternate atlas at the moment, but we are working on it. -Lilla On Tue, 28 Jan 2014, Mher Alaverdyan wrote: They are 2 - 8 years old

Re: [Freesurfer] Destrieux Atlas with Kid brains

Hi, What is the age range of your subjects? Lilla On Tue, 28 Jan 2014, Mher Alaverdyan wrote: Hi all, I just wanted to know if it is acceptable to use the Destrieux atlas in FS for parcellation of brain images of pre-adolescents. If not this atlas, then which would be a recommended

Re: [Freesurfer] Destrieux Atlas with Kid brains

I would say that for 5-8 the atlas would probably work. Below 5 I would be skeptical. There is no alternate atlas at the moment, but we are working on it. -Lilla On Tue, 28 Jan 2014, Mher Alaverdyan wrote: They are 2 - 8 years old. On Tue, Jan 28, 2014 at 11:46 AM, Lilla Zollei lzol

Re: [Freesurfer] MNC label to Freesurfer

Hi Caspar, One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes. --replace V1 V2 : replace voxels=V1 with V2 For label descriptions you can loook up

Re: [Freesurfer] MNC label to Freesurfer

each label in the MNC file to a new Freesurfer label file. Caspar 2014/1/6 Lilla Zollei lzol...@nmr.mgh.harvard.edu Hi Caspar, One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option

Re: [Freesurfer] problem with createMorph

Hi Andre, I posted the below on Monday on the list: The boost library is installed by default on CentOS platforms. If a user gets the libboost error then they are using a different platform which doesn't have boost installed by default. On RedHat systems libboost can be installed by typing

Re: [Freesurfer] affine registration with mri_robust_register

mri_robust_register --help You would need to use the --affine flag. Lilla On Fri, 22 Nov 2013, Nathaniel Reynolds wrote: Hi all, I can't find any explanation of how to perform an affine registration with mdi_robust_register. Could someone please explain? Thanks, Nathaniel

Re: [Freesurfer] mri_mi

It is not checked in as of now to the FS distribution. I can send it to you. On Fri, 22 Nov 2013, Nathaniel Reynolds wrote: Hi again, Does anybody know about a function called mri_mi? I have someone else's script that seems to utilize it, but I can't seem to access it myself. Thanks,

Re: [Freesurfer] CVS registration questions

Hi Tommi, I am preparing to CVS register 30+ subjects to improve FSL probabilistic tractography alignment across subjects. First, thanks for a really cool tool! Then, I have some questions: 1. mri_cvs_register step1 is spherical registration. However, I have already run FS5.3 recon-all

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