Re: [Freesurfer] voxel of different size

2015-07-11 Thread Bruce Fischl
Hi Sandro can you clarify what you mean? Do you want to run recon-all on each one separately? That would be fine. Or do you mean somehow average all the different res volumes into a single recon? cheers Bruce On Sat, 11 Jul 2015, Sandro Marini wrote: Dear FreeSurfer experts, we have col

Re: [Freesurfer] Freesurfer Digest, Vol 137, Issue 13

2015-07-11 Thread Bruce Fischl
, Sandro Message: 11 Date: Sat, 11 Jul 2015 10:04:20 -0400 (EDT) From: Bruce Fischl Subject: Re: [Freesurfer] voxel of different size To: Freesurfer support list Message-ID:         Content-Type: text/plain; charset="utf-8" Hi Sandro

Re: [Freesurfer] R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

2015-07-12 Thread Bruce Fischl
you can change formats with mri_convert: mri_convert vol.nii.gz vol.mgz but you shouldn't need to - all our tools will read nifti just fine. Doug's question was whether your mask was in the right coordinates, regardless of whether it was in mgz or nifti. cheers Bruce On Sun, 12 Jul 2015,

Re: [Freesurfer] Computing SA from an older FS version

2015-07-12 Thread Bruce Fischl
Hi Niels is that the entire error? Does it not say what volume produces the error? That was a bug we had briefly some time ago, but I didn't think it made it into anything we released. If you can track down which volume is causing this problem you can just load it into matlab with load_mgh.m

Re: [Freesurfer] Computing SA from an older FS version

2015-07-13 Thread Bruce Fischl
vard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: zondag 12 juli 2015 16:44 To: Freesurfer support list Subject: Re: [Freesurfer] Computing SA from an older FS version   Hi Niels   is that the entire error? Does it not say what volume produces the error? Th

Re: [Freesurfer] Computing SA from an older FS version

2015-07-13 Thread Bruce Fischl
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: maandag 13 juli 2015 14:46 To: Freesurfer support list Subject: Re: [Freesurfer] Computing SA from an older FS version   Hi Niels   the matlab commands should be:   >> [v, M,mr] = load_mgh('wm.mgz') ; >&g

Re: [Freesurfer] Correction with white-matter-points

2015-07-14 Thread Bruce Fischl
Hi Pawel does this happen in both versions? If so, upload a bad subject and we will take a look cheers Bruce On Tue, 14 Jul 2015, Wrobel, Pawel wrote: > Dear FreeSurfer Team! > > We have a question concerning corrections with white-matter-points. > > We are currently working on a T1 data set. A

Re: [Freesurfer] mris_anatomical_stats giving segmentation faults for certain subjects

2015-07-15 Thread Bruce Fischl
can you run mris_info on /scratch/lfs/aoshea/testAndrew/dotsonFSprocessed//EX03/surf/rh.white and/or view it in freeview to make sure it isn't corrupted? On Wed, 15 Jul 2015, O'Shea,Andrew wrote: Hello all, I am having an issue where the mris anatomical stats command is failing and only prin

Re: [Freesurfer] mris_anatomical_stats giving segmentation faults for certain subjects

2015-07-15 Thread Bruce Fischl
icode1 talairach_flag 0 rescale 0.00 nvertices 106524 nfaces 213044 total_area 69696.328125 group_avg_vtxarea_loaded 0 avgvtxarea 0.654278 avgvtxdist 0.886314 stdvtxdist 0.266572 vtx0xyz 18.017620 -83.093475 36.833847 [aoshea@gator1 ~]$ On 7/15/15, 12:05 PM, "Bruce

Re: [Freesurfer] (no subject)

2015-07-16 Thread Bruce Fischl
Hi Amirhossein we will reformat them all to 1mm iso during recon-all. Hopefully those differences are small enough not to cause a bias. cheers Bruce On Thu, 16 Jul 2015, amirhossein manzouri wrote: Hi FS, MR images of two of my subjects in a group have been acquired with different T1 pro

Re: [Freesurfer] Regarding post contrast T1 MPRAGE (Gadolinium)

2015-07-19 Thread Bruce Fischl
ay 13, 2015 at 8:38 AM, Bruce Fischl wrote: the gad will make the dura more likely to be segmented as wm and might require more manual interventions, but if you are willing to put in the time it should still be usable. cheers Bruce On Wed, 13 May 2015, Santosh

Re: [Freesurfer] tksurfer.bin: tnl/t_vertex.c:413 error | load patch

2015-07-19 Thread Bruce Fischl
Hi Itamar no, I never got to the bottom of this. Zeke: do you know anything about it? Bruce On Sat, 18 Jul 2015, Itamar Kahn wrote: Dear Bruce et al., I encountered the dreadful t_vertex assertion failed error. I’ve seen on the list it showed up a while ago. Did you figure out which packag

Re: [Freesurfer] Correction with white-matter-points

2015-07-20 Thread Bruce Fischl
(PNL) > Brigham and Women's Hospital > > > > Message: 6 > Date: Tue, 14 Jul 2015 11:33:57 -0400 (EDT) > From: Bruce Fischl > Subject: Re: [Freesurfer] Correction with white-matter-points > To: Freesurfer support list > Message-ID: > > Content-Type: TEX

Re: [Freesurfer] make_average_subject for subcortical volumes in children

2015-07-20 Thread Bruce Fischl
Hi Kristi yes, that is correct. Everything is stored in native space and all processing is done there until you start doing group-level stuff cheers Bruce On Fri, 17 Jul 2015, Kristi Griffiths wrote: Dear FS experts,   I am new to freesurfer and have a few basic questions.   I have

Re: [Freesurfer] How to deal with the distortions of EPI images when applying the parcellated results of T1 images?

2015-07-21 Thread Bruce Fischl
Hi Bingjiang did you acquire any field maps? If so, you can them to undistort the EPIs cheers Bruce On Tue, 21 Jul 2015, Bingjiang Lyu wrote: > Dear all, > I've got the automaticlly parcellated 'aparc.a2009s+aseg.nii' file for > individual T1 image, and I want to calculate functional connectiv

Re: [Freesurfer] mri_watershed mask and skull surfaces

2015-07-21 Thread Bruce Fischl
Hi Sam if you want us to help you, you need to provide us with the full command line and screen output (at least!) cheers Bruce On Tue, 21 Jul 2015, Sam Zorowitz wrote: Hi all, I am using mri_watershed to create skull surfaces for a cohort of subjects for whom we were unable to collect a F

Re: [Freesurfer] How to deal with labels and structural data

2015-07-21 Thread Bruce Fischl
Hi Silas what do you want to do with the labels? As for whether to do it on fsaverage or individuals, you could start with fsaverage and map it to your other subjects and see how accurate it looks cheers Bruce On Tue, 21 Jul 2015, Silas wrote: > Dear Freesurfer team, > I've created my own lab

Re: [Freesurfer] mri_convert command line did not provide output file

2015-07-22 Thread Bruce Fischl
Hi Stefano can you send us the command that was run and the full output? Bruce On Wed, 22 Jul 2015, std...@virgilio.it wrote: > Hi list, > > mri_convert command line did not provide output file. > > This error was produced during the first computations of trac-all -prep > command line. > >

Re: [Freesurfer] How to deal with labels and structural data

2015-07-22 Thread Bruce Fischl
Hi Silas I think we already provide the information you want as we tabulate the thickness of the different parcels in the various files in each subject's stats dir. If you want to do the same thing with a different set of labels draw the labels on fsaverage, use mri_label2label to map them to

Re: [Freesurfer] Subcortical segmentation necessary steps

2015-07-22 Thread Bruce Fischl
Hi Tony if you run recon-all it will do everything needed. You could stop after mri_ca_label I suppose, but then you won't be able to use the surfaces to correct white matter and cortex. cheers Bruec On Wed, 22 Jul 2015, Tony Koroulakis wrote: > Dear Freesurfer Team, > > I am inquiring as t

Re: [Freesurfer] hello freesurfer developer~

2015-07-23 Thread Bruce Fischl
actors) : diagnosis continuous (covariate) : age , Left-Lateral-Ventricle --- which one click before analyze? 2015-04-05 21:41 GMT+09:00 Bruce Fischl : I'm glad it worked out Bruce On Sun, 5 Apr 2015, A-reum M

Re: [Freesurfer] Overlapping of aparc.annot labels

2015-07-23 Thread Bruce Fischl
HI Alessia you can turn the aparc file into separate labels using mri_annotation2label, then load different parcels as individual labels cheers Bruce On Thu, 23 Jul 2015, Alessia Sarica wrote: > Dear all, > > this is to know if you can suggest me the right way for visualizing on > FreeSurfer

Re: [Freesurfer] Question about pial surface correction through Freesurfer

2015-07-23 Thread Bruce Fischl
Hi Kalyan usually improving the wm surfaces results in improved pial surfaces. If not, it typically means something went wrong. If you upload a subject and email me and Ani the coordinates of a spot (or spots) you are having trouble, we will take a look cheers Bruce On Thu, 23 Jul 2015, Trip

Re: [Freesurfer] Question about pial surface correction through Freesurfer

2015-07-24 Thread Bruce Fischl
Hi Antonin that's a good point and something we probably need to fix. Bruce On Fri, 24 Jul 2015, Antonin Skoch wrote: > Dear Kalyan, > > do you use standard pial surface reconstruction via T1 images, or optional > pial > surface refinement with T2/FLAIR images? > > I had similar problems wit

Re: [Freesurfer] Question about pial surface correction through Freesurfer

2015-07-24 Thread Bruce Fischl
p.s. although in this case I think it won't hurt to always pass that parameter since it is only used for the flair/pial stuff On Fri, 24 Jul 2015, Antonin Skoch wrote: > Dear Kalyan, > > do you use standard pial surface reconstruction via T1 images, or optional > pial > surface refinement with

Re: [Freesurfer] pial surface from one hemisphere is crossing the surface of other hemishpere

2015-07-24 Thread Bruce Fischl
Hi Antonin not sure - if you upload the subject I'll take a look Bruce On Fri, 24 Jul 2015, Antonin Skoch wrote: > Dear experts, > > I came several times across the situation when pial surface from one > hemisphere > is crossing the surface of other hemishpere (see the attached screenshot). Is

Re: [Freesurfer] white surface "leaking" from the brain

2015-07-24 Thread Bruce Fischl
Hi Antonin I think that the current flair/pial stuff will correct small errors in the wm placement, but this one is probably too large and is really a skull stripping problem. Have you tried gcuts? If the dura is attached to the wm then the mris_make_surfaces step will not usually fix it. sorr

Re: [Freesurfer] Create brain outline from pial surface

2015-07-24 Thread Bruce Fischl
you could try binarizing the brainmask.mgz cheers Bruce On Fri, 24 Jul 2015, Liang Wang wrote: Hi folks, I would like to create a brain outline based on the generated pial surface. This outline will completely cover the whole cortex (ignoring gyrus and sulcus info) and is treated as a brain o

Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes

2015-07-24 Thread Bruce Fischl
Hi Caspar we tried to replicate this and couldn't. Can you upload the subject(s) involved in this and send us the exact command line that shows the problem? cheers Bruce On Fri, 24 Jul 2015, Caspar M. Schwiedrzik wrote: -- Forwarded message -- From: Caspar M. Schwiedrzik

Re: [Freesurfer] Create brain outline from pial surface

2015-07-24 Thread Bruce Fischl
you can use mri_morphometry and use the close operation to get rid of some holes On Sat, 25 Jul 2015, Liang Wang wrote: Thanks Bruce. I applied mri_binarize to brainmask.mgz with specified threshold and got many holes in the mask. In addition, brainmask.mgz includes the cerebellum. I would like

Re: [Freesurfer] [FreeSurfer] add to color lut for aparc+aseg.mgz

2015-07-24 Thread Bruce Fischl
yes, I guess so On Fri, 24 Jul 2015, joseph veliz wrote: > We need to subdivide regions of the VentralDC that would carry onto the > aparc+aseg.mgz. > > Would this involve just editing the aseg.mgz? > > > On Fri, Jul 24, 2015 at 9:27 AM, Douglas Greve > wrote: > For surface ROIs, you'll

Re: [Freesurfer] [FreeSurfer] multicore recons

2015-07-24 Thread Bruce Fischl
Hi Joseph if you have lots to get through you might be better off running two with 4 cores at a time. Speed increase is pretty good through 4 last time Nick tested, but then the benefits fall off a bit Bruce On Fri, 24 Jul 2015, joseph veliz wrote: > What is the best set up to utilize the mul

Re: [Freesurfer] hello freesurfer developer~

2015-07-26 Thread Bruce Fischl
Maybe Zeke or Ruopeng know? > On Jul 26, 2015, at 5:17 PM, A-reum Min wrote: > > Hi, Bruce > > When i use a Qdec, this message(12.png) show up.. > How can i solve this problem? > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl : >> 1. No, each subject has a differe

Re: [Freesurfer] smoothing

2015-07-27 Thread Bruce Fischl
Hi Eric the optimal smoothing kernel more or less matches the size of the effect, so it's impossible to say a priori. A bigger kernel is better if there is more widespread subtle thinning cheers Bruce On Mon, 27 Jul 2015, Erik Lindberg wrote: > Dear freesufers, > I quick question about smoot

Re: [Freesurfer] QA measures mgz

2015-07-27 Thread Bruce Fischl
it depends on which gm you are looking at. For cortex you can use the brain.mgz, for any subcortical structure you can use the norm cheers Bruce On Mon, 27 Jul 2015, Jacek Manko wrote: I can't recommend anything in that case, since I am just relying on available, but very scanty documentat

Re: [Freesurfer] Recon-all error

2015-07-27 Thread Bruce Fischl
hmmm, that usually means you ran out of memory, which is surprising given that that step doesn't take very much. Were there other jobs running on the same machine? On Mon, 27 Jul 2015, Park, Jung Mi wrote: Hello Freesurfer expert I got an error message while running recon-all.   1) subject na

Re: [Freesurfer] recon-all error_cannot find or read transforms/talairach.m3z

2015-07-27 Thread Bruce Fischl
there is probably an error before that. Can you send the entire recon-all.log? On Mon, 27 Jul 2015, Park, Jung Mi wrote: Hello Freesurfer expert Running recon-all abruptly stopped with this error message at NMR center;  mri_ca_register -invert-and-save transforms/talairach.m3z  Loading, Inve

Re: [Freesurfer] dev version of mri_ca_label memory leak?

2015-07-29 Thread Bruce Fischl
Hi Chris if you send me all the inputs to mri_ca_label and your exact command line I'll see if I can replicate it and either fix it or send you a new version. Or you can try the current dev version and see if it fixes things cheers Bruce On Wed, 29 Jul 2015, Chris Adamson wrote: Devs,  

Re: [Freesurfer] recon-all -white does not respect wm edits

2015-07-29 Thread Bruce Fischl
Hi Antonin if it is correct in the orig.nofix but not correct in the orig that means it was an incorrectly fixed topological defect that you need to manually correct. I'll see if we can find someone here to take a look. Bruce On Wed, 29 Jul 2015, Antonin Skoch wrote: Dear experts, during

Re: [Freesurfer] wm parcellation freesurfer

2015-07-29 Thread Bruce Fischl
Hi Owais do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use mris_divide_parcellation or mris_make_face_parcellation to subdivide or make an isotropic finer scale one if you want. I believe that you can then create a new aparc+aseg from one of those and then the wmparc from that to g

Re: [Freesurfer] Increasing thickness threshold?

2015-07-29 Thread Bruce Fischl
yes, specify -max on the command line to mris_thickness and mris_make_surfaces (you can do this in recon-all with expert options) cheers Bruce On Wed, 29 Jul 2015, Jesse Bledsoe wrote: > Hi FreeSurfer community, > > I would like to see if FreeSurfer could be used to improve clinical detect

Re: [Freesurfer] dev version of mri_ca_label memory leak?

2015-07-30 Thread Bruce Fischl
-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, 30 July 2015 12:03 AM To: Freesurfer support list Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak? Hi Chris if you send me all the inputs to mri_ca_label and your

Re: [Freesurfer] Repost: problem with mri_label2label - large amount of holes

2015-07-30 Thread Bruce Fischl
Hi Caspar the dev version of label2label doesn't have this problem. If you let us know your hardware/software environment Zeke can get you a new binary that should fix this issue cheers Bruce On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote: Hi Bruce and Doug, thanks for looking into th

Re: [Freesurfer] Total intracranial volumes

2015-07-30 Thread Bruce Fischl
Hi Andre why would changing the surfaces affect ICV? We estimate ICV using Randy Buckner's method of looking at the determinant of the Talairach transform, which is totally insensitive to the surface placement. cheers Bruce p.s. I think it's more common to include ICV as a regression factor

Re: [Freesurfer] Help with Freesurfer preprocessing pls

2015-07-30 Thread Bruce Fischl
Hi Lena you need to run the hippocampal subfield code. Depending on what version you are running it could mean adding something like: -hippocampal-subfields- and removing the -autorecon-all cheers Bruce On Thu, 30 Jul 2015, Lim, Lena wrote: Dear Freesurfer experts,   My colleague (who

Re: [Freesurfer] Help

2015-07-31 Thread Bruce Fischl
Hi Katherine you can try changing permissions on the .license file if you own it: chmod +w $FREESURFER_HOME/.license if you don't you'll have to get the owner (or a sysadmin) to change it cheers Bruce On Fri, 31 Jul 2015, Petrilli Paolino, Katherine wrote: Hi,  I've been having problem

Re: [Freesurfer] increasing thickness threshold

2015-07-31 Thread Bruce Fischl
mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics:    1. Re: recon-all -white does not respect wm edits (Antonin Skoch)    2. Re: wm parcellation freesu

Re: [Freesurfer] Atlas conversion to NIFTI

2015-07-31 Thread Bruce Fischl
HI Pantea our atlases contain a lot more information than that and can't easily fit into nifti (e.g. the Markov probabilities). Plus the fact that the gcs is on the surface and not in 3D (it is on the surface of the sphere) cheers Bruce On Fri, 31 Jul 2015, Pantea Moghimi wrote: Hi, I wa

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

2015-07-31 Thread Bruce Fischl
Hi Jon you need to send us the exact command line you are using for the conversion and the counting cheers Bruce 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

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

2015-07-31 Thread Bruce Fischl
why are you specifying the output orientation? That is probably causing resampling On Fri, 31 Jul 2015, Jonathan Plasencia wrote: > > We are using the following line: > > > mri_convert aseg.mgz aseg.nii --out_orientation RAS > > > > Best, > > Jonathan Plasencia > Graduate Student > NSF G

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

2015-07-31 Thread Bruce Fischl
ellow School of Biological and Health Systems Engineering Arizona State University Email: jplas...@asu.edu Phone: (480)861-7017 On Fri, Jul 31, 2015 at 12:54 PM, Bruce Fischl wrote: why are you specifying the output orientation? That is probably causing resampling On F

Re: [Freesurfer] mris_register problem: "No such file or directory"

2015-08-02 Thread Bruce Fischl
hmm, something seems to be wrong maybe the the ?h.sphere. Can you try recreating it cheers Bruce On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: Hi all, I received an error in one of the steps of recon-all. The error is "No such file or directory" at the end of one of the registration processe

Re: [Freesurfer] mris_register problem: "No such file or directory"

2015-08-02 Thread Bruce Fischl
the same, I am guessing that any non-deterministic process would have the same output. Is there a a way to automatically know if there was a problem in the sphere creation? Cheers. 2015-08-02 16:27 GMT+01:00 Bruce Fischl : hmm, something seems to be wrong maybe the the ?h.sphere. Can

Re: [Freesurfer] Help with Freesurfer preprocessing pls

2015-08-03 Thread Bruce Fischl
  Thanks,   Lena     -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 30 July 2015 18:02 To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls   Hi Le

Re: [Freesurfer] Help with Freesurfer preprocessing pls

2015-08-03 Thread Bruce Fischl
ginal Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 03 August 2015 15:38 To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls Hi Lena those aren't files that you

Re: [Freesurfer] Help with Freesurfer preprocessing pls

2015-08-03 Thread Bruce Fischl
d.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 03 August 2015 16:04 To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls no! Don't delete those files - we need them. Just don't include them in your for loop cheers Bruce

Re: [Freesurfer] Help with Freesurfer preprocessing pls

2015-08-03 Thread Bruce Fischl
subjects I have so far ? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 03 August 2015 16:41 To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls I

Re: [Freesurfer] wm parcellation freesurfer

2015-08-03 Thread Bruce Fischl
original T1 MRI? If it is possible to do so that would be nice, otherwise I will probably try to run the entire recon -all with the new voxel size. Thanks, Owais   On Wed, Jul 29, 2015 at 11:25 AM, Bruce Fischl wrote: Hi Owais do you mean the wmparc.mgz or the aparc+aseg.mgz?

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

2015-08-03 Thread Bruce Fischl
Jonathan Plasencia Graduate Student NSF Graduate Research Fellow School of Biological and Health Systems Engineering Arizona State University Email: jplas...@asu.edu Phone: (480)861-7017 On Fri, Jul 31, 2015 at 12

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

2015-08-03 Thread Bruce Fischl
le is based off the mgz file. If this is the case then yes to your first question). I'll send a mgz file and its stats file directly to your personal email in a minute: fis...@nmr.mgh.harvard.edu Best, Jon On Mon, Aug 3, 2015 at 1:18 PM, Bruce Fischl wrote: and you are saying that ase

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

2015-08-04 Thread Bruce Fischl
minute: >> >> fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu> >> >> Best, >> >> Jon >> >> On Mon, Aug 3, 2015 at 1:18 PM, Bruce Fischl >> mailto:fis...@nmr.mgh.harvard.edu>> wrote: >> >> and you are saying tha

Re: [Freesurfer] Weird Freesurfer results

2015-08-04 Thread Bruce Fischl
Hi Brent are you saying you just multiplied the gray matter intensities by some scale factor (>1)? Bruce On Tue, 4 Aug 2015, Brent Womble wrote: Hi everyone, I've been making synthetic brains to test how Freesurfer handles various structural changes. One of the changes I'm testing is increa

Re: [Freesurfer] Weird Freesurfer results

2015-08-04 Thread Bruce Fischl
k=padarray(k,padsize_pre,1,'pre'); %Restrict the kernel to the gray mask b=k.*c1; b(~c1)=1; %%Apply the kernel to the original image c=b.*a; %Write to .nii raw.img=c; save_nii(raw,[pwd,'/', num2str(i), '/dense-sy

Re: [Freesurfer] Weird Freesurfer results

2015-08-04 Thread Bruce Fischl
a uniform darkening of the gray matter. On Tue, 4 Aug 2015, Brent Womble wrote: Yes, I'm multiplying the image intensities by a scaling factor. Sorry if that wasn't clear. -Brent On Aug 4, 2015 12:09, "Bruce Fischl" wrote: Hi Brent a quick look and it seems that

Re: [Freesurfer] ThickAvg of specific structures

2015-08-04 Thread Bruce Fischl
Just doing those structures should be fine Bruce > On Aug 4, 2015, at 10:46 PM, prasser wrote: > > Hi, > > > > If I am only interested in the gm thickness (ThickAvg) of a specific > structure/s (e.g. precentral) is it sufficient to only QC these specific > structures/s or does the wm and

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

2015-08-05 Thread Bruce Fischl
Hi Saeed if you specify -w to mris_inflate or mris_sphere it will save snapshots of the process every nth iteration cheers Bruce On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: > Hello, > > Since surface deformation from WM to inflated surface is a gradual process, > I assume that in

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

2015-08-05 Thread Bruce Fischl
you can use convert to take the multiple tiff files that are written and output a dynamic gifti On Wed, 5 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: > Thanks Bruce, and Is there an easy way to make a movie of this deformation? > > On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl

Re: [Freesurfer] ID-swapping freesurfer data?

2015-08-05 Thread Bruce Fischl
the easiest thing to do is to read them into matlab and write them back out. I think that strips all the tags (which is where the subject name is stored) On Wed, 5 Aug 2015, Nate Vack wrote: Thanks! One complication I'm seeing is that when I uncompress, say, an .mgz file, the old subject numbe

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

2015-08-05 Thread Bruce Fischl
Will it be captured from a specified perspective and 1 tiff for each volume?And these tiff files will be combined to generate animated gif? What is "dynamic gifti"? On Wed, Aug 5, 2015 at 3:08 PM, Bruce Fischl wrote: you can use convert to take the multiple tiff files that a

Re: [Freesurfer] Fornix Segmentation

2015-08-06 Thread Bruce Fischl
Hi Maryam try specifying -f on the mri_cc command line (as the first option) cheers Bruce On Thu, 6 Aug 2015, Syeda Maryam wrote: > Hi everyone, > > So I've been going through the list trying to see if someone has encountered > the same problem as me with regards to segmentation of the fornix

Re: [Freesurfer] Fornix Segmentation

2015-08-06 Thread Bruce Fischl
s it possible to separate the two? > Thanks in advance! > > Regards, > Maryam > > > > On Thursday, August 6, 2015 1:22 PM, Bruce Fischl > wrote: > > > Hi Maryam > > try specifying -f on the mri_cc command line (as the first option) > > cheers > B

Re: [Freesurfer] how to obtain sulcal depth in a given region for a specific subject

2015-08-06 Thread Bruce Fischl
sure, you can use mris_anatomical_stats with the label (-l) and specify sulc instead of thickness on the command line Bruce On Thu, 6 Aug 2015, Yang, Daniel wrote: > Dear FreeSurfer Experts, > > Is there a way to obtain sulcal depth in a given region (label) for a > particular subject? > > Man

Re: [Freesurfer] Weird Freesurfer results

2015-08-06 Thread Bruce Fischl
r gyrus dataset first because it was simplest. On Tue, Aug 4, 2015 at 12:58 PM, Bruce Fischl wrote: What you really want to simulate is an underlying geometric deformation (like atrophy) that gets propagated through an image formation model to create an atrophic image. I don

Re: [Freesurfer] how to obtain sulcal depth in a given region for a specific subject

2015-08-06 Thread Bruce Fischl
; GrayVol ThickAvg ThickStd > > When sulc is used instead of thickness, do you know what the meaning of > these three variables is changed to? > > Many thanks, > Daniel > > On 8/6/15, 1:35 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Bruce Fischl" fi

Re: [Freesurfer] Label or Overlay of Surface files

2015-08-06 Thread Bruce Fischl
no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, etc...) On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when

Re: [Freesurfer] Label or Overlay of Surface files

2015-08-06 Thread Bruce Fischl
load them as "curvature" files cheers Bruce On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: And are they treated as label files (e.g. lh.aparc.annot ) in the label directory? And how they can be added to the tksurfer snapshot procedure? On Thu, Aug 6, 2015 at 4:04 PM, Br

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

2015-08-06 Thread Bruce Fischl
here? I set w to 5 and > all of the iterations are spheres! > > Thanks, > Saeed > > On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl > wrote: > Hi Saeed > > if you specify -w to mris_inflate or mris_sphere it will > save snapshots > of

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

2015-08-07 Thread Bruce Fischl
. On Aug 6, 2015 7:45 PM, "Bruce Fischl" wrote: yes, because it is unfolding on the sphere to recover metric properties. -w 1 gives you every iteration. You will need to show curvature or you won't see anything On Thu, 6 Aug 2015, Saeed Mahdiza

Re: [Freesurfer] mri_deface

2015-08-07 Thread Bruce Fischl
Hi Jurgen why not just use the defaced T1 as a mask for the DTI? Bruce On Fri, 7 Aug 2015, Jürgen Hänggi wrote: Dear FS experts I have to anonymize T1-w. and DTI images. I run mri_deface for T1-w. images successfully,  but I am wondering whether there is any easy way to also deface DTI imag

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

2015-08-07 Thread Bruce Fischl
information for mris_sphere? This page seems to e incomplete in that aspect. Many Thanks, Saeed On Fri, Aug 7, 2015 at 10:36 AM, Bruce Fischl wrote: Hi Saeed we normally project onto the sphere, but if you want to generate a movie to show the idea you can give mris_sphere the flag -i

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

2015-08-07 Thread Bruce Fischl
save your time for more technical questions. Documentation doesn't correlate with how great FS and it's support community is. On Fri, Aug 7, 2015 at 11:11 AM, Bruce Fischl wrote: I guess only by looking at the code. We have tried to flesh out most of the documentation but ha

Re: [Freesurfer] options for 7T images...

2015-08-09 Thread Bruce Fischl
Hi Gonzalo Jon and Kyoko (both ccd) have put together a 7T stream, and should be able to help you out cheers Bruce On Sat, 8 Aug 2015, Gonzalo Rojas Costa wrote: Hi:   Must I use any recon-all option for 7T images ?...   Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory f

Re: [Freesurfer] uploading a surface in freeview

2015-08-09 Thread Bruce Fischl
Hi Carina it should be something like: freeview -f /lh.inflated:overlay=mc-z.abs.2.sig.cluster.mgh assuming mc-z.abs.2.sig.cluster.mgh is in your current directory cheers Bruce On Sun, 9 Aug 2015, car...@van-vlodrop.de wrote: Hi Lilla, I still have the problem to display my surface creat

Re: [Freesurfer] options for 7T images...

2015-08-09 Thread Bruce Fischl
sorry, had an old address for Kyoko On Sun, 9 Aug 2015, Bruce Fischl wrote: Hi Gonzalo Jon and Kyoko (both ccd) have put together a 7T stream, and should be able to help you out cheers Bruce On Sat, 8 Aug 2015, Gonzalo Rojas Costa wrote: Hi:   Must I use any recon-all option for

Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s

2015-08-09 Thread Bruce Fischl
Hi Andre it's up to you. The aparc and .aparc.DKTatlas40 are probably pretty similar, although we haven't looked at the .aparc.DKTatlas40 much. The aparc.a2009s contains more, smaller parcels, and so is probably less reliable but might correspond more closely to an anatomical hypothesis you h

Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s

2015-08-10 Thread Bruce Fischl
001/t1.mgz, -1) > could not open file" > > Any suggestions? > Thank you. > AS > ___ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu

Re: [Freesurfer] creating a new subject directory using imported data from existing subject directory

2015-08-10 Thread Bruce Fischl
Hi Emma can you clarify? Did you process one subject in a directory then overwrite it with a second? If so you probably can't recover it without rerunning recon-all. cheers Bruce On Mon, 10 Aug 2015, Emma Thompson wrote: > Hi, > I'm re-posting my query in case it got buried on the listserve

Re: [Freesurfer] ID-swapping freesurfer data?

2015-08-10 Thread Bruce Fischl
yes, it should Bruce On Mon, 10 Aug 2015, Nate Vack wrote: On Fri, Aug 7, 2015 at 2:45 PM Douglas N Greve wrote:   On 08/07/2015 03:11 PM, Nate Vack wrote: > Thanks. Any other file types I should look for tags in? I think the surfaces have the subject name imbedded in them.

Re: [Freesurfer] [FreeSurfer] Axis of Alignment

2015-08-11 Thread Bruce Fischl
Hi Joseph, no it shouldn't matter to us what the angle is as long as it's in approximately the right orientation. You could reorient the volumes in freeview if you wanted, but I don't think it's necessary cheers Bruce On Mon, 10 Aug 2015, fmri wrote: > Hello FreeSurfer experts, > > When MRI

Re: [Freesurfer] mri_vol2surf: convert stats volume to surface

2015-08-11 Thread Bruce Fischl
Hi Vincent you aren't creating a surface - you are creating a scalar overlay on the surface. Try something like: freeview -f lh.inflated:overlay=output.mgh not that the MNI transform doesn't do a very good job aligning cortex so the results will spread over adjacent gyri and such cheers Br

Re: [Freesurfer] uploading a surface in freeview

2015-08-11 Thread Bruce Fischl
g and endling you told me, freeview opens with the error message 'failed to load surface' and in the command field it says 'MRISread failed'. Do you have any idea of how it is possible to avoid this error?   Best regards, Carina   Gesendet: Sonntag, 09. August 2015 um 16:33 Uh

Re: [Freesurfer] creating a new subject directory using imported data from existing subject directory

2015-08-11 Thread Bruce Fischl
to redo anything (e.g., recon-all), does that sound correct to you? Thanks so much for your help! On Mon, Aug 10, 2015 at 3:44 PM, Bruce Fischl wrote: Hi Emma can you clarify? Did you process one subject in a directory then overwrite it with a second? If so you pro

Re: [Freesurfer] [FreeSurfer] Axis of Alignment

2015-08-11 Thread Bruce Fischl
Ruopeng should be able to help you out cheers Bruce On Tue, 11 Aug 2015, fmri wrote: > Is there a wiki instruction block on how to reorient all volumes? > > Thanks > > On Aug 11, 2015, at 6:13 AM, Bruce Fischl wrote: > >> Hi Joseph, >> >> no it shouldn'

Re: [Freesurfer] [FreeSurfer] Axis of Alignment

2015-08-11 Thread Bruce Fischl
oops, had a typo in Ruopeng's address. On Tue, 11 Aug 2015, Bruce Fischl wrote: > > Ruopeng should be able to help you out > > cheers > Bruce > On Tue, 11 Aug 2015, fmri wrote: > >> Is there a wiki instruction block on how to reorient all volumes? >> >

Re: [Freesurfer] uploading a surface in freeview

2015-08-12 Thread Bruce Fischl
wrote:   Hi Bruce,   I send you a screenshot of my command field with my command line and the following error message. Thank you very much for your help. Carina Gesendet: Dienstag, 11. August 2015 um 16:54 Uhr Von: "Bruce Fischl" An: "Freesurfer support list" Betreff: Re: [F

Re: [Freesurfer] Exporting the Hippocampus

2015-08-13 Thread Bruce Fischl
Hi Chester the voxel coords reflect positioning in the scanner and so there is a lot of variability in them depending on landmarking, head size, etc... cheers Bruce On Thu, 13 Aug 2015, Chester Dolph wrote: I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used m

Re: [Freesurfer] Loading .w surface overlay in Freeview

2015-08-13 Thread Bruce Fischl
can you use vol2surf to generate a .mgz/.mgh file instead? We have deprecated the use of .w files On Thu, 13 Aug 2015, Ivan Alvarez wrote: > Dear all, > > I am wondering if there is a facility for loading .w overlay files in > Freeview? In the surface section of the GUI, the overlay tab is for

Re: [Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer

2015-08-13 Thread Bruce Fischl
Hi Jan have you asked the HCP/Wash U group? I bet that they would know. Maybe Mike Harms or Matt Glasser can chime in? Bruce On Thu, 13 Aug 2015, Jan Willem Koten wrote: Dear ladies and possibly gentlemen as well,   I have got a rather nasty question. I would like to import the followi

Re: [Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer

2015-08-13 Thread Bruce Fischl
FreeSurfer formats), however I don’t provide Caret support either having not used it in years (I can be more helpful with Connectome Workbench stuff). Donna on the Caret list can perhaps provide further help. Peace, Matt. On 8/13/15, 12:12 PM, "Bruce Fischl" wrote: Hi Jan have you asked th

Re: [Freesurfer] registering 2 scans

2015-08-14 Thread Bruce Fischl
Hi Matt can you tell us what your goal is for this analysis? You could use the longitudinal tools depending on what you are up to cheers Bruce On Fri, 14 Aug 2015, Hibert, Matthew Louis wrote: Hi Freesurfers, I've scanned the same subject with 2 different head coils and reconstructed the

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