Re: [Freesurfer] Infant MRI segmentation

2015-01-28 Thread Lilla Zollei
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] applyMorph to 3d voxel coordinate list

2015-02-04 Thread Lilla Zollei
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 Greenber

Re: [Freesurfer] recon-all dimensions

2015-02-05 Thread Lilla Zollei
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] topology defect in freesurfer

2015-02-06 Thread Lilla Zollei
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 g

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

2015-02-25 Thread Lilla Zollei
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 wo

Re: [Freesurfer] mri_cvs_register using high resolution images

2015-05-06 Thread Lilla Zollei
Hi Celine, The m3z morph encodes a sptial transformation between two particular coordinate systems. When you use mri_vol2vol below, the original space is not the same as for your input volume used to be and that is why the volumes are not in correspondence. Could you compute the registration

Re: [Freesurfer] mri_cvs_register using high resolution images

2015-05-07 Thread Lilla Zollei
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 sugg

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

2015-06-26 Thread Lilla Zollei
t; Fischl [fis...@nmr.mgh.harvard.edu] > Gesendet: 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 > i

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

2015-07-31 Thread Lilla Zollei
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

2015-07-31 Thread Lilla Zollei
Email: jplas...@asu.edu > Phone: (480)861-7017 > > On Fri, Jul 31, 2015 at 12:31 PM, Lilla Zollei > wrote: > >       Hi Jon, > >       What is the exact command that you used for the below described >       conversion? >

Re: [Freesurfer] CVS question

2016-07-14 Thread Lilla Zollei
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 w

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

2016-09-30 Thread Lilla Zollei
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 Freesur

Re: [Freesurfer] Registration

2016-11-03 Thread Lilla Zollei
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 t

Re: [Freesurfer] Infant brain atlas

2016-12-15 Thread Lilla Zollei
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 http

Re: [Freesurfer] mri_cvs_register

2016-12-26 Thread Lilla Zollei
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 this

Re: [Freesurfer] createMorph & applyMorph: unexpected results

2017-01-11 Thread Lilla Zollei
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 FreeSurfe

Re: [Freesurfer] T1 data on 1yr-old subjects

2013-10-10 Thread Lilla Zollei
Hi Jim, Using the current FS recon pipeline with your data is indeed not feasible. We are in the process of creating another pipeline geared towards that age range. Lilla On Thu, 10 Oct 2013, Alexopoulos, Dimitrios wrote: > Just wondering if anyone has attempted to process T1-mpr data for a

Re: [Freesurfer] New Atlas Creation

2013-10-10 Thread Lilla Zollei
Hi Liv, What you are asking for is quite ambitious. As you have noticed, most of the image processing tools fail on the infant data sets as they are usually of much lower SNR, they have changing GM/WM contarst, higher noise and a much smaller anatomy. So it is not only a question of creating

Re: [Freesurfer] CVS registration questions

2013-10-28 Thread Lilla Zollei
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-a

Re: [Freesurfer] affine registration with mri_robust_register

2013-11-22 Thread Lilla Zollei
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

2013-11-22 Thread Lilla Zollei
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. > >

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

2013-11-25 Thread Lilla Zollei
This is a bit delayed response (my apologies) to an earlier question to 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

Re: [Freesurfer] problem with createMorph

2013-11-27 Thread Lilla Zollei
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 t

Re: [Freesurfer] MNC label to Freesurfer

2014-01-06 Thread Lilla Zollei
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 $FREESURFER_HOME/FreeSurferColorLU

Re: [Freesurfer] MNC label to Freesurfer

2014-01-06 Thread Lilla Zollei
mply like to convert each label in the MNC file to a new Freesurfer > label file. > Caspar > > > > 2014/1/6 Lilla Zollei > > Hi Caspar, > > One thing you can do, if you have the label correspondences between > your lables and the FS ones, is to use mri_

Re: [Freesurfer] Destrieux Atlas with Kid brains

2014-01-28 Thread Lilla Zollei
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 a

Re: [Freesurfer] Destrieux Atlas with Kid brains

2014-01-28 Thread Lilla Zollei
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,

Re: [Freesurfer] Destrieux Atlas with Kid brains

2014-02-03 Thread Lilla Zollei
ced at any 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 Ala

[Freesurfer] setting the useRealRAS bit

2014-02-09 Thread Lilla Zollei
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, L

Re: [Freesurfer] setting the useRealRAS bit

2014-02-09 Thread Lilla Zollei
m, but I 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 M

Re: [Freesurfer] setting the useRealRAS bit

2014-02-10 Thread Lilla Zollei
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: > >> &

Re: [Freesurfer] reconstruction problem with pediatric images

2014-03-19 Thread Lilla Zollei
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 ge

Re: [Freesurfer] reconstruction problem with pediatric images

2014-03-21 Thread Lilla Zollei
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 : Hi Francesco, How old are

Re: [Freesurfer] reconstruction problem with pediatric images

2014-03-24 Thread Lilla Zollei
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzol...@nmr.mgh.harvard.edu] Sent: Friday, March 21, 2014 10:12 AM To: Francesco Baldacchini Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer

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

2014-05-07 Thread Lilla Zollei
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 it

Re: [Freesurfer] bring volumes to fsaverage space

2015-10-30 Thread Lilla Zollei
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: http://surfer.nmr.mgh.harvard.edu/pu

Re: [Freesurfer] register image to mni152

2016-01-17 Thread Lilla Zollei
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 regist

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

2016-01-21 Thread Lilla Zollei
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, Abbaye de Saint Jacut, Brittany, France, June 1

Re: [Freesurfer] mri_cvs_register : output

2016-03-21 Thread Lilla Zollei
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  co

Re: [Freesurfer] Using digital tablet pen

2016-03-22 Thread Lilla Zollei
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, Ma

Re: [Freesurfer] (no subject)

2013-03-21 Thread Lilla Zollei
Hi Martina, What was the command that you ran when executing mri_cvs_register. The default outpur directory is $SUBJECTS_DIR/$subject/cvs. The help alos explains how you can change that directory. --Lilla On Thu, 21 Mar 2013, Bruce Fischl wrote: > mri_vol2vol or mri_convert can apply the .m3

Re: [Freesurfer] Admin: Please unsubscribe this email address

2013-03-27 Thread Lilla Zollei
Hi Maish, You can just go to https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer and unsubscribe your email address. Lilla On Wed, 27 Mar 2013, Dalwani, Manish wrote: > Hello Admin, > > Please unsubscribe this email address. > > Regards, > Manish >

Re: [Freesurfer] advice for subcortical Freesurfer processing of 2 year old brains

2013-04-02 Thread Lilla Zollei
Hi Josh, We do not yet have a publicly available atlas for that population. We are working on it though and will announce it as soon as it is ready. Lilla On Tue, 2 Apr 2013, Joshua Lee wrote: > The aseg has shown poor performance in my sample. Are there settings, > atlases, etc, available t

Re: [Freesurfer] mris_resample: Command not found.

2013-05-28 Thread Lilla Zollei
Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote: Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3.  When I ran mri_cvs_check, my feedback was I needed to find "mri_cvs_register.settings.txt

Re: [Freesurfer] mris_resample: Command not found.

2013-06-03 Thread Lilla Zollei
ur >>> $FREESURFER_HOME/bin directory: >>> >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample >>> >>> Feel free to contact me if you have any additional questions/issues. >>> >>> -Zeke >>> >>>

Re: [Freesurfer] R: R: Re: R: Re: Tracula

2013-06-06 Thread Lilla Zollei
HI, A patch is now available for the "mris_resample : Command not found" error you encountered. Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample --Lilla On Thu, 6 J

Re: [Freesurfer] CVS and group analysis

2013-06-09 Thread Lilla Zollei
Hi, Can you be more specific? What files / volumes do you want to compute a group average of? On Sun, 9 Jun 2013, Fernando Valle-Inclán wrote: Hi freesurfers,    After doing cvs registration, how can I make a group average? Is fsaverage OK? Thanks _

Re: [Freesurfer] CVS and group analysis

2013-06-09 Thread Lilla Zollei
m talking about "final_CVSmorphed_tocvs_avg35.norm.gz"Thanks for the very prompt reply F 2013/6/9 Lilla Zollei Hi, Can you be more specific? What files / volumes do you want to compute a group average of? On Sun, 9 Jun 2013, Fernando Valle-Inclán wrote: Hi freesurfers,    After doing

Re: [Freesurfer] mri_cvs_register std:: bad_alloc

2013-07-09 Thread Lilla Zollei
Hi Marcel, You would ned at least twice as much. Also, is there a specific reason for you to use the --m3d flag? That will result in writing out uncompressed morph files which will take up a lot of space. Lilla On Tue, 9 Jul 2013, Marcel Falkiewicz wrote: Dear FreeSurfers,  I'm trying to us

Re: [Freesurfer] application of mri_cvs_register question

2013-07-09 Thread Lilla Zollei
Hi, What type of registration file do you have representing the diff2anat transformation? With mri_vol2vol you can use many different types of transformations, if you switch the --reg flag to --xfm, --fsl or --lta, for example. Lilla On Mon, 8 Jul 2013, Hoptman, Matthew wrote: Hi all,

Re: [Freesurfer] application of mri_cvs_register question

2013-07-10 Thread Lilla Zollei
diff2anat.bbr.mat Matrix from regfile: -0.001 0.972 -0.234 -3.311; -0.001 0.234 0.972 69.949; 0.000 0.000 0.000 1.000; 0.000 0.000 0.000 0.000; Best, Matt -Original Message- From: Lilla Zollei [mailto:lzol...@nmr.mgh.harvard.edu] Sent: Wednesday, July 10, 2013 6:07 PM To

Re: [Freesurfer] cvs_avg35

2013-07-29 Thread Lilla Zollei
It should be in your $FREESURFER_HOME/subjects directory. Lilla On Sun, 28 Jul 2013, SHAHIN NASR wrote: Hi,    Would you tell me where I can find cvs_avg35 brain template.   -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School _

Re: [Freesurfer] cvs_register then mri_vol2vol

2013-08-06 Thread Lilla Zollei
Hi Daniel, You need to specify the full path to the target volume, the subject id is not sufficient. It should be somthing like this: $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz Lilla On Tue, 6 Aug 2013, Barron, Daniel S wrote: > Hi Freesurfers (Lilla), > > I'm running v5.1.0 o

Re: [Freesurfer] mri_cvs_register for EPI

2013-08-08 Thread Lilla Zollei
Hi Marcel, First, you will find a lot of details about the usage of mri_cvs_register if you use the --help flag in the terminal. See detailed responses to your questions below:  I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. Ho

Re: [Freesurfer] mri_cvs_register for EPI

2013-08-08 Thread Lilla Zollei
idea... Can you think of any solutions to this issue? Best regards,  Marcel 2013/8/8 Lilla Zollei Hi Marcel, First, you will find a lot of details about the usage of mri_cvs_register if you use the --help flag in the terminal. See detailed responses to your questions below

Re: [Freesurfer] aparc+aseg labels

2012-06-05 Thread Lilla Zollei
Hi Cyrus, You can run the following script: compute_label_volumes.csh It will list all the labels that are in your segmentation file (and also tell you the number of voxels colored by this label and th etotal volume). Lilla On Tue, 5 Jun 2012, Sarosh, Cyrus wrote: Hello,   I was hopin

Re: [Freesurfer] mri_cvs_register - use of wmparc instead of aseg

2013-03-14 Thread Lilla Zollei
Hi Daniel. > i'm currently applying mri_cvs_register and I'm very happy with the nice > results. Congratulation for this very clever approach. However, some data > sets which I work on have still aseg.mgz which are not segmented > appropriately. As far as I understand aseg.mgz is not redefined

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

2017-01-26 Thread Lilla Zollei
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 (w

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

2017-02-01 Thread Lilla Zollei
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, Lilla Zollei  wrote: Hi

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

2017-02-01 Thread Lilla Zollei
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 to

Re: [Freesurfer] mri_cvs_register error : PETSC Error

2017-02-20 Thread Lilla Zollei
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 error : PETSC Error

2017-02-20 Thread Lilla Zollei
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 wrote: Hi Bhavana, How much memory are you allocating to this process? Lilla On Mon, 20 Feb 2017, Bhavana

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

2017-02-20 Thread Lilla Zollei
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 Don

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

2017-02-20 Thread Lilla Zollei
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] Output from mri_cvs_register

2017-02-20 Thread Lilla Zollei
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 combined_tocvs_

Re: [Freesurfer] mri_cvs_register error : PETSC Error

2017-02-21 Thread Lilla Zollei
[linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png] On Mon, Feb 20, 2017 at 4:43 PM, Lilla Zollei wrote: Hi Bhavana, We recommend to assign about 35GB of RAM on our cluster nodes for this operation. I am not sure how that compares to your VB. Lilla

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

2017-02-28 Thread Lilla Zollei
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] apply CVS morph to a list of coordinates

2017-03-02 Thread Lilla Zollei
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] Haskins Pediatric Atlas use in FS

2017-05-26 Thread Lilla Zollei
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 Pediatric

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

2017-06-15 Thread Lilla Zollei
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 Free

Re: [Freesurfer] recon-all on newborn

2017-07-04 Thread Lilla Zollei
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 image

Re: [Freesurfer] recon-all on newborn

2017-07-05 Thread Lilla Zollei
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 July 2

Re: [Freesurfer] recon-all on newborn

2017-07-06 Thread Lilla Zollei
sy 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] Pediatric Atlas/Template

2017-07-17 Thread Lilla Zollei
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 child

Re: [Freesurfer] Freesurfer pipeline for infant

2017-07-17 Thread Lilla Zollei
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 car

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

2017-07-28 Thread Lilla Zollei
-- 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 cytoarchitecture using diffusi

[Freesurfer] postdoc ad

2017-08-07 Thread Lilla Zollei
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-compa

[Freesurfer] Open position at Lausanne University Hospital: research and development engineer (fwd)

2017-08-08 Thread Lilla Zollei
FYI -- Forwarded message -- Date: Mon, 7 Aug 2017 12:54:29 + From: Meritxell Bach Cuadra To: Meritxell Bach Cuadra Subject: Open position at Lausanne University Hospital: research and development engineer Dear colleague, we are looking for a research and development e

Re: [Freesurfer] Newborn MRI segmentation

2017-09-21 Thread Lilla Zollei
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 recommend?

Re: [Freesurfer] QC on CVS registration

2017-11-22 Thread Lilla Zollei
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] neonatal brain

2017-11-27 Thread Lilla Zollei
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, Dijksho

Re: [Freesurfer] neonatal brain

2017-11-28 Thread Lilla Zollei
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] free surfer v5 & 6

2017-12-13 Thread Lilla Zollei
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 respe

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

2018-01-03 Thread Lilla Zollei
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] Nonlinear CVS registration into average brain rdinates

2018-01-10 Thread Lilla Zollei
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 cod

Re: [Freesurfer] no skullstrip

2018-01-12 Thread Lilla Zollei
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 surfer

[Freesurfer] about Rahul Desikan

2018-06-14 Thread Lilla Zollei
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): https://www.washingtonpost.com/ne

Re: [Freesurfer] Infant atlas/pipeline

2018-07-09 Thread Lilla Zollei
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 infa

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

2014-07-01 Thread Lilla Zollei
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] Jacobian mri_cvs_register

2014-07-10 Thread Lilla Zollei
Hi Andre You can run: mri_jacobian -tm3d <3d morph> --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? Regards, Andre Santos Ribeiro

Re: [Freesurfer] Jacobian mri_cvs_register

2014-07-11 Thread Lilla Zollei
AM, André Ribeiro wrote: Thank you! Didn't realized that function existed. Regards, Andre Santos Ribeiro On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei wrote: Hi Andre You can run: mri_jacobian -tm3d <3d morph> --Lilla On Thu,

Re: [Freesurfer] Jacobian mri_cvs_register

2014-07-11 Thread Lilla Zollei
ase out the tm3d format. Lilla On Fri, Jul 11, 2014 at 3:11 PM, Lilla Zollei 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 er

Re: [Freesurfer] uploading a surface in freeview

2014-07-16 Thread Lilla Zollei
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

[Freesurfer] RA position available in Neuroimaging of Multiple Sclerosis

2014-07-25 Thread Lilla Zollei
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] Jacobian mri_cvs_register

2014-08-05 Thread Lilla Zollei
ke here? Sorry 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 wrote: Hi, First, in the mri_cvs_register I kept all the files and therefore the "combined_toIBSR_02_elreg_after

Re: [Freesurfer] Fwd: Jacobian mri_cvs_register

2014-08-06 Thread Lilla Zollei
]  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 wrote: Hi Andre, What do you mean by they "do not seem to match voxel-wise"? Are they of

Re: [Freesurfer] Fwd: Jacobian mri_cvs_register

2014-08-06 Thread Lilla Zollei
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 wrote: Hi Andre, The jacobian field is computed in the coordinate

Re: [Freesurfer] dt_recon error

2014-08-11 Thread Lilla Zollei
Hi Rito. It is not finding information about the gradient table that was used for the acquisition. If you have that information you can use the below option to manually include it --b bvals bvecs If you do not you could try using load_dicom in order to grab that information. Lilla On Mon,

Re: [Freesurfer] mri_cvs_register

2014-09-10 Thread Lilla Zollei
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 entere

Re: [Freesurfer] mri_cvs_register

2014-09-10 Thread Lilla Zollei
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 https://mail.nmr.mgh.harvard.edu/mailman/li

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