Re: [Freesurfer] gnumeric file

Hi Caroline the data are in native space. Summary statistics means e.g. the volume of the left hippocampus. You don't need any registration algorithm for this type of thing - you just tabulate it across subjects cheers Bruce On Thu, 17 Mar 2016, Caroline Beelen wrote: Hi Bruce, Thank

Re: [Freesurfer] WM edit, remove GM bright rim

Hi Min unfortunately there's not much we can do as these artifacts make the gray matter look just like white matter. Do you see this in many subjects? sorry Bruce On Thu, 17 Mar 2016, Min Liu wrote: Dear Bruce,  Many thanks for looking into this. I tried to post orig.mgz to the mailing

Re: [Freesurfer] FreeSurfer 6.0

Hi Elisabeth we don't have an exact date yet, but have finished our code modifications (hopefully!) and are in the process of freezing a version after which we will run a set of tests and hopefully release it cheers Bruce On Wed, 16 Mar 2016, Elisabeth Paul wrote: > Dear ladies and

Re: [Freesurfer] error - mri_nu_correct.mni

Hi Douglas, I have done this but I got the following error: [hwilson@nig05 ~]$ cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri [hwilson@nig05 mri]$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

[Freesurfer] GM mask to native T1

I am attempting to align the GM mask (lh.ribbon.mgz) to the T1 in native space. I see this thread that states this command is the correct way: mri_label2vol --seg lh.ribbon.mgz --temp rawavg.mgz --o ribbon-in-rawavg.mgz --regheader ribbon.mgz from:

Re: [Freesurfer] Replacing / turning off denoising filter

Thanks! Just FYI - we applied newer version of NLME from Pierrick Coupé before running freesurfer and it greatly improved segmentation results. On Wed, Mar 16, 2016 at 3:47 PM Bruce Fischl wrote: > Hi Mojmir > > we don't apply mri_nlfilter by default so there is no

[Freesurfer] HIRING: Research Assistant

Hello, The Houston Methodist Research Institute is hiring for a research assistant position. Please see the attached document for details. Please also note that candidates must be able to work in the city of Houston day-to-day. If you are interested in applying, please follow the instructions

Re: [Freesurfer] mris_flatten error: bad vertex

Dear. Bruce. Thanks a lot for your help! I attached the tar.gz file for mri below. If you need anything more, let me know. Thanks, Ji Won​ replay06_mri.tar.gz ​ 2016-03-17 11:40 GMT-04:00 Bruce Fischl

[Freesurfer] Anterior to Posterior Length

Good morning, I apologize if this email was sent out twice. I would like to use anterior to posterior length as a covariate in my DTI analysis. Is there an easy way to obtain this information for each subject? Thank you, Heather ___ Freesurfer

[Freesurfer] ID not identified on surface file

Dear Friends, I need to 3D render the AAL parcellation volume, with labels (in annotation file) for each ROI. My AAL volume is on MNI152 standard space, with 2mm 91x109x91, as well my results volumes. I used the following command to generate my surface files from my AAL volume. mri_vol2surf

Re: [Freesurfer] aparc stats volume outputting area instead

Hi Doug, Many thanks indeed: everything working fine now. BW clare From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: 16 March 2016 14:53 To:

Re: [Freesurfer] Hippocampal subfield segmentation with T1

Hi Xiaowei, this was my mistake when I wrote the article in the wiki. The images do not need to be in the same orientation (I already changed this in the wiki). They need to be coarsely registered in physical coordinates (i.e., the need to look approximately registered when you open them in

[Freesurfer] Regarding: running lgi with freesurfer dev6 and matlab2016a

Dear freesurfer expert Marie, I am trying to run lgi after doing recon-all. I am getting stuck with an error. Just wanted to know if freesurfer dev6 is compatible with newest Malta 2016a version. Thanks and regards, Sampada Predoctoral student KGMU, Lucknow India -- Sampada Sinha

Re: [Freesurfer] Anterior to Posterior Length

Hi Heather the anterior/posterior length of each tract you mean? Or the length of the entire hemi? Bruce On Wed, 16 Mar 2016, Heather Acuff wrote: Good morning, I apologize if this email was sent out twice.  I would like to use anterior to posterior length as a covariate in my DTI analysis. 

Re: [Freesurfer] Smoothing at FWHM (Qdec)

Hi Martin there is no easy answer to this question. Basically, the optimal smoothing filter depends on the size of the effect you are looking for (the so-called "matched-filter theorem"). IN general, if you have bigger groups of subjects and/or expect focal differences use a smaller kernel.

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

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

[Freesurfer] preproc-sess in longitudinal stream

Dear. Freesurfer experts. Hi. How are you? I have dataset where a single subject was scanned twice on different days. I ran recon-all in logitudinal stream (cross, base, long). The recon-all -base gave me the within-subject template and the recon-all -long gave me the directory in the format of

Re: [Freesurfer] aparc stats volume outputting area instead

There is not actually a "-meas" option. It should be either " -m volume" or " --measure=volume". Strange, it should have exited with an error but some reason it did not and used area as the default. On 3/16/16 10:27 AM, Clare Loane wrote: Hi Doug, I am using version 5.3 and the terminal

[Freesurfer] mri_glmfit-sim ( cluster wise analysis)

Dear FS experts, I ran cortical thickness analysis as previously explained in Wiki : Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 1. My data is previously cached so I ran the command : mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage

[Freesurfer] Reg: Correcting Defect error

Dear Freesurfer experts, I have been running freesurfer for a patient data, and have to find this retesselalation of defect. I have successful with some data but for some others it looks frozen even after 7 days. Would it be possible to please have a look and help me out? Also, how could I pass

Re: [Freesurfer] Replacing / turning off denoising filter

Hi Mojmir we don't apply mri_nlfilter by default so there is no need to turn it off. You are welcome to try it out. It implement some nonlinear filters including what is now called nonlocal means as described in this paper:

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

Can you send me what dt_recon prints to the screen when your run the command below? On 3/15/16 11:40 PM, Jasmin Alves wrote: Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 INFO: SUBJECTS_DIR is

Re: [Freesurfer] tksurfer

it looks like the cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indicates that is where the peak of the cluster is and does not mean that the cluster is confined to that ROI On 3/16/16 9:43 AM, John Anderson wrote: Dear experts,

Re: [Freesurfer] FWHM file not found

Many thanks! > On Mar 16, 2016, at 15:18, Marie Schaer wrote: > > > You still have to “smooth” even if you choose fwhm=0 to project the data in > the fsaverage space. > > So if I were you I would start with fwhm=5mm, check in the qdec console what > is the final fwhm

Re: [Freesurfer] Problems with file un qdec analysis

that's what I thought ! Thanks a lot for your help ! Best regards ! Lisa 2016-03-15 17:31 GMT+01:00 Douglas N Greve : > you cannot have more than two levels of a factor in qdec. You can use > the "command line" stream. See the wiki > > On 03/14/2016 06:52 AM, Lisa

Re: [Freesurfer] FWHM file not found

Thanks for que quick answer, Marie. If I got right, I should either not smooth it after mri_preproc (no mri_surf2surf) or do it with kernels < 5mm, and that should make to FMHM fall below 30. Am I correct? Thanks, Pedro. On Wed, Mar 16, 2016 at 3:03 PM, Marie Schaer wrote:

Re: [Freesurfer] tksurfer

Thank you doug, Please what do you suggesst me to do? Is this related to something wrong in the analysis?   Bests, John   Sent: Wednesday, March 16, 2016 at 10:42 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer it

Re: [Freesurfer] AAL 3D rendering with subcorticals

Did you check the volume to verify that at least one voxel has an index = 75 ? On 3/19/16 10:43 AM, João V. Dornas wrote: Dear friends, I am following this procedures to plot a 3D rendering of the AAL volume (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27707.html). My

Re: [Freesurfer] cannot allocate memory

that's going to create a pretty big volume as it will map your functional time course to a 256^3 float volume. If you have 100 time points, then that will be about 7G. On 3/16/16 3:27 PM, Ehsan Tadayon wrote: Hi Bruce, Thanks for your response. I'm using : freesurfer version:

Re: [Freesurfer] Replacing / turning off denoising filter

that's interesting. Is it open source? If so, can you point us at it? Maybe someone should compare it to the version I wrote 20 years ago :) On Fri, 18 Mar 2016, Mojmír Vinkler wrote: Thanks! Just FYI - we applied newer version of NLME from Pierrick Coupé before running freesurfer and it

Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

I did more digging around and came up with a procedure. Please let me know if it would cause any problems. Looking at the contents of the X.mat files (which contain the predictors), it appears that the betas are indeed arranged as c1 d1 c2 d2… I also found that isxconcat-sess requires the

[Freesurfer] AAL 3D rendering with subcorticals

Dear friends, I am following this procedures to plot a 3D rendering of the AAL volume (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27707.html). My problem is the following. When I execute this command: mri_cor2label --i lh.Colin27_aal2std.mgh --id 75 --l lh_Pallidum_L

Re: [Freesurfer] gnumeric file

On 3/16/16 6:52 AM, Caroline Beelen wrote: Hi FS team, Sorry for these rather basic questions… I'm not sure whether the gnumeric file is an ascii file (see mails below). Attached you'll find the file. It seems the case when you open it in the terminal screen that the nr's look fine (with

Re: [Freesurfer] FreeSurfer 6.0

Although it should be mentioned that outputs (even of subfields) are going to change due to differences in the regular freesurfer processing, as the subfields stream builds upon the regular FS stream. Best, Martin On 03/16/2016 10:52 AM, Eugenio Iglesias wrote: > I only changed some details

Re: [Freesurfer] FreeSurfer 6.0

I only changed some details (e.g., temporary directories) that do not affect the output. Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Bruce Fischl"

Re: [Freesurfer] Regarding: running lgi with freesurfer dev6 and matlab2016a

Sorry for the typos...its Matlab 2016a version I meant! On Wednesday, March 16, 2016, Dr Sampada Sinha wrote: > Dear freesurfer expert Marie, > > I am trying to run lgi after doing recon-all. I am getting stuck with an > error. Just wanted to know if freesurfer dev6 is

[Freesurfer] Per-vertex regression model

Hello FS experts, I would like to correlate for each vertex 2 anatomical variables (for example cortical thickness and surface area), i.e. doing a vertex-wise correlation between 2 maps for a cohort of subjects. Maybe it is possible with the command line mri-glmfit and with the argument "--pvr

[Freesurfer] Hippocampal subfield segmentation with T1

Dear Freesurfer expert, I am using Freesurfer V6.0 beta version to run the hippocampal subfield segmentation with 2 inputs, a standard T1 and a high resolution T2. Below are the details about the 2 images. T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8) T2: resolution:

Re: [Freesurfer] LUT in ImageJ

Hi Kaiming yes, that file should exist in $FREESURFER_HOME. Not sure about ImageJ - you might want to ask them cheers Bruce On Wed, 16 Mar 2016, Kaiming Yin wrote: > Dear guys, > Is there a file of "FreeSurferColorLUT.txt" available in the Freesurfer > folders, or should I copy/paste the texts

Re: [Freesurfer] Skull strip

Hi Uli that looks like a pretty dramatic failure for the surfaces even without considering the skull stripping problem. There are some expert options that can improve this a ton (e.g. mris_make_surfaces -wlo and such). If you would prefer you can upload the whole subject (tarred and gzipped )

[Freesurfer] surface based analysis using FA maps

Hi Doug, I would like to run surface based analysis using FA maps. I am not exactly sure that what I am doing is totally right specially step 2 . I used the following commands: 1. I registered the FA maps to T1 using the command: bbregister --s bert --mov dtifit_FA.nii --bold

Re: [Freesurfer] group analysis all measures same results

Dear Douglas, 1) Does this beta version of FS 6 (freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015.tar.gz) also have problems with the individual data analysis or the volumetric group analysis, e.g. the files in the stats/ folder for each subject? 2) So could I use the results of these

Re: [Freesurfer] Replacing / turning off denoising filter

Hi Bruce, I have applied one of his denoising algorithms on my high resolution datasets and also got very nice results. I used it on a single subject only, however, this could be beneficial for the upcoming hires pipeline to account for lower SNR. You can find his algorithms and

Re: [Freesurfer] Anterior to Posterior Length

Thank you very much! Heather On Wed, Mar 16, 2016 at 11:24 AM, Bruce Fischl wrote: > I see. I don't think we generate that by default. If you have a bunch of > subjects I guess you could great a single vertex label at the frontal pole > and another at occipital pole

Re: [Freesurfer] Anterior to Posterior Length

I see. I don't think we generate that by default. If you have a bunch of subjects I guess you could great a single vertex label at the frontal pole and another at occipital pole on fsaverage, then map each of them to each subjects and compute the distance between them. That will be a rough

Re: [Freesurfer] mri_robust_register question

Hi Ji-Won, Why not just input both T1s to recon-all it will motion correct and average and then all of your functionals will be registered to the same FS data? hth d On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang wrote: > Dear. All. > > Hi. How are you? > > It might be a

Re: [Freesurfer] FreeSurfer 6.0

Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and ran the HSF method successfully. Have they retracted that version? best, Alan On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl wrote: > actually there is no beta yet, but hopefully within a

Re: [Freesurfer] FreeSurfer 6.0

Hi Elizabeth: I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great. Beta is available for download. Here is the URL: https://surfer.nmr.mgh.harvard.edu/fswiki/Download best, Alan On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul < elisabeth.p...@student.uva.nl> wrote: >

Re: [Freesurfer] aparc stats volume outputting area instead

Hi Doug, I am using version 5.3 and the terminal output does not state an error (below) and the file is created (attached) but as you will see, it is the area measurements which are output. dcnmac75:Freesurfer clare$ aparcstats2table --subjects CON_001 CON_002 CON_003 CON_004 CON_006

Re: [Freesurfer] Hippocampal subfield segmentation with T1

Hi Xiaowei you can try mri_robust_register --cost nmi or --cost mi, then give the resulting transform to mri_convert -at transform.lta -rl T2.mgz The "-rl T2.mgz" tells mri_convert to "reslice like" the T2, so they will have the same geometry. You can also try mri_coreg if you like instead

Re: [Freesurfer] mri_robust_register question

Hi, when using recon-all for this, the right way would be to run both images through the longitudinal stream. This will create a mid-space template and map both time points to it. That space can also be used as target for the functional data. That way you stay unbiased. Probably the potential

[Freesurfer] mris_flatten error: bad vertex

Dear. Freesurfer experts. Hi. I'm having a problem with mris_flatten (version 5.3.0) Could you please help me fix this problem? My command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat It returns the error:

Re: [Freesurfer] Replacing / turning off denoising filter

thanks Falk Bruce On Fri, 18 Mar 2016, Falk Lüsebrink wrote: Hi Bruce,   I have applied one of his denoising algorithms on my high resolution datasets and also got very nice results. I used it on a single subject only, however, this could be beneficial for the upcoming hires pipeline to

Re: [Freesurfer] gnumeric file

Hi Bruce, Thank you very much! :) I think somethings wrong with gnumeric indeed just discovered that gedit works fine. As for 3, that would mean that the data are not in native space? I'm trying to understand this concept of "summary statistics" :-). Thanks again in advance. Caroline

Re: [Freesurfer] FreeSurfer 6.0

that's a good point On Wed, 16 Mar 2016, Martin Reuter wrote: > > Although it should be mentioned that outputs (even of subfields) are > going to change due to differences in the regular freesurfer processing, > as the subfields stream builds upon the regular FS stream. > > Best, Martin > > > On

[Freesurfer] WM edit, remove GM bright rim

Dear Freesufer users, We have some T1 images having a rim of bright signal in the GM at some spots like the one showing in the attached Figure 1. The WM surface goes out to include this bright signal and the cortex ends up artificially thin. We followed the standard WM edit procedure, which is

Re: [Freesurfer] FreeSurfer 6.0

actually there is no beta yet, but hopefully within a week or so On Wed, 16 Mar 2016, Alan Francis wrote: Hi Elizabeth: I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great. Beta is available for download. Here is the URL:

Re: [Freesurfer] gnumeric file

Dear FS I typed in: aparcstats2table --hemi lh --meas thickness --subjects A01_T1 > A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed by) > gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, it > generated the table attached in the previous mail. Thank you

Re: [Freesurfer] cannot allocate memory

Hi Bruce, Thanks for your response. I'm using : freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS X Yosemite 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm using: mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o func.anat.nii.gz Thanks in

Re: [Freesurfer] Extremely small numbers of extracted pial surface area

Dear Freesurfer experts, I am reposting my question from early this week since it is not answered. Any help much appreciated. My question is about the measure of pial surface area. Following a group comparison and correction in QDEC, I found a significant cluster (size: 760mm^2) when

Re: [Freesurfer] Replacing / turning off denoising filter

Here's another implementation https://github.com/Inria-Visages/Anima-Public/wiki/Denoising-tools#nl-means-denoising. We'll be comparing different methods and throw in both your and the newer version and see if there's any significant difference at all. On Fri, Mar 18, 2016 at 10:38 PM Bruce

Re: [Freesurfer] WM edit, remove GM bright rim

Hi Min that looks like it might be a normalization problem. Can you post the orig.mgz and see what it looks like? Is there a bright rim in it also? cheers Bruce On Wed, 16 Mar 2016, Min Liu wrote: Dear Freesufer users, We have some T1 images having a rim of bright signal in the GM at some

Re: [Freesurfer] mri_robust_register question

Hi. Daniel. How are you? Thanks for your reply. That should be another option for me! Thanks, Ji Won 2016-03-17 15:16 GMT-04:00 dgw : > Hi Ji-Won, > > Why not just input both T1s to recon-all it will motion correct and > average and then all of your functionals will be

Re: [Freesurfer] "Bump" - Fwd: lGI value is aberrantly high and misalignment fix

Hi Marco, It’s pretty strange because from the recon-all.log you sent, the first LGI process went fine (line 14584 and 19329 for the right and left hemispheres, on Dec 15). Then you don’t run anything else on the surfaces and just reprocess the exact same LGI process for the same subject (Dec

Re: [Freesurfer] gnumeric file

Hi Bruce, Ok, very clear. Thank you! :-) Regards, Caroline -Oorspronkelijk bericht- Van: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl Verzonden: donderdag 17 maart 2016 15:47 Aan: Freesurfer support list

Re: [Freesurfer] Reading values from overlays with PETcoreg

Dear Doug, Is it possible to use BP SUVR PET that have been registered to T1 for this gtmseg workflow? You mentioned that the mean TAC should be used as the input. 2 quick questions: What's mean TAC and why? Thanks. Best Wishes, Elijah ___ Freesurfer

[Freesurfer] mri_glmfit

Hi Experts, What is the meaning of this error as an output of the command mri_glmfit   Found 0 voxels in mask ERROR: no voxels found in the mask   make sure at least one voxel has a non-zero value for each input   in other words what are therrors that can lead to such like error message    

Re: [Freesurfer] tksurfer

Hi John I do not know anything about the error that you are getting but I was also having some problems with tksurfer and was told by Dr. Fischl that this viewer is no longer being updated and that it would be best to try freeview. Did you give this a go? best wishes Trisanna -- Ph.D.

[Freesurfer] Post-doctoral position available – Human Neurocognitive Aging

Post-doctoral position – Human Neurocognitive Aging The Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Division of Psychiatric Neuroimaging (PI: Arnold Bakker, Ph.D.) has a vacancy for 1-2 postdoctoral scholars to perform federally-funded research

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

No, I mean that when the command is run, it will print a lot of text to the screen. I want to know what that text is. You can run the following command and send me the dng.log file dt_recon --debug --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log On

Re: [Freesurfer] gnumeric file

Hi Caroline have you looked at the lh.aparc.thickness.table? If it is correct then it is something strange with gnumeric and I'm not sure we are qualified to help you. As for 3, the tables contain summary stats and so don't need to be mapped into any common space. cheers Bruce On Thu,