Re: [Freesurfer] cannot find qdec file

no worries! sadly, though, deleting the empty line wasn't the answer to the problem :( Cheers, Clara - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 4. August 2015 20:43:47 Betreff: Re: [Freesurfer] cannot find qdec file oops, sorry fo

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

Hi Bruce, Doug, and Zeke, just checking back regarding the dev version for mri_label2label. Do you have a build that works on MAC OS 10.9.5 Mavericks? So far, we have been using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0. Thank you, Caspar 2015-08-03 6:40 GMT-04:00 Caspar M. Schwiedrzik

Re: [Freesurfer] registering NHP data

Awesome that you guys are working a parcellation! In the meantime, if I wanted to try to use the atlases you suggested, how would I go about processing the data? Is there documentation I can follow? Thanks so much, Mia From: MCLAREN, Donald [mclaren.don...@gm

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

Hello Caspar, I did a quick test and it appears the new dev version of mri_label2label is still compatible with the version of 5.1 that you have. Please use the following link to download it and also please make sure to back up the version you already have. ftp://surfer.nmr.mgh.harvard.edu/pub

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

Hi Zeke, Thank you, we will give it a try! Caspar On Wednesday, August 5, 2015, wrote: > Hello Caspar, > > I did a quick test and it appears the new dev version of mri_label2label > is still compatible with the version of 5.1 that you have. Please use the > following link to download it and also

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

Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of "Analyzing the Individual Subject " tutorial session (sli

Re: [Freesurfer] qdec problem

The error message is: ERROR: The stats file /Users/i_geschwind/Desktop/qdec_test/CDPAD02WJD_recon/stats/aseg.stats is not found or is too small to be a valid statsfile Have you checked this stat file? It is a text file, so you can just look inside it. On 08/04/2015 10:19 PM, geschwind2013 wrot

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

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

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 wrote: > 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,

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

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 > wrote: >

[Freesurfer] Exception caught for createMorph

Hi, I'm trying to apply a transform that was generated between a native subject's T1 and the cvs_avg35_inMNI152 brain. Per the instructions on the mri_cvs_register page, I ran the transformation, but did not save the .fullCVSmorph.t3md file, so I'd like to regenerate it. Here's my command for doin

[Freesurfer] mkanalysis-sess, timewindow

Hi, I set timewindow to 10 in the mkanalysis-sess. When I loaded Xtmp.mat in to maltlab, then plot(flac.ev(2).Xirf), the size of the flac.ev(2).Xirf is 20 points, which is corrected because of psdwin is [0 40 2]. Should the psdwin be [0 10 2]? No matter what value I put in to timewindow, t

Re: [Freesurfer] surface reconstruction and quality control

Hi Emma, I'd exclude it and similar images. Or if you have a motion estimate of those subjects (e.g. via adjacent fMRI or diffusion scans), you could use motion as a covariate in your statistics. Motion does bias measurements (smaller cortical GM volume), see e.g. here: http://dx.doi.org/10.1

[Freesurfer] mri_convert IMA to MGZ

Hi freesurfers, I want to localize electrode locations from a NHP CT scan, am i able to do that with tkmedit without coregistering first? I don't need all the parcellations of a specific atlas, just the RAS coordinates. Also, the CT images are IMA files. Is there a way to convert from IMA to MG

Re: [Freesurfer] ID-swapping freesurfer data?

Thanks! One complication I'm seeing is that when I uncompress, say, an .mgz file, the old subject number is still embedded in some text near the end of the file*. Since we want to change these ID numbers for de-identification purposes, we'd need to change them there, too. Is there a way to either

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

I am a bit confused, "mri_convert" is basically used to convert 3D models (e.g. .inflate file types) to tiff images? 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,

Re: [Freesurfer] surface reconstruction and quality control

Thanks Martin, I will exclude this subject from my analyses. On Wed, Aug 5, 2015 at 4:18 PM, Martin Reuter wrote: > Hi Emma, > > I'd exclude it and similar images. Or if you have a motion estimate of > those subjects (e.g. via adjacent fMRI or diffusion scans), you could use > motion as a covari

Re: [Freesurfer] surface reconstruction and quality control

Hi Emma, Martin, I'd like to offer a different perspective.  Based on what you showed, I thought that the motion related ringing wasn't too bad, and I'd expect that FS would handle that data quite well, which is what you indicated was indeed the case.  If we all started excluding data of th

Re: [Freesurfer] ID-swapping freesurfer data?

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

not mri_convert, convert. And sorry, I mean a dynamic gif: man convert NAME convert - convert between image formats as well as resize an image, blur, crop, despeckle, dither, draw on, flip, join, re-sample, and much more. SYNOPSIS convert [input-options] input-file [outpu

[Freesurfer] Head Motion -- was: surface reconstruction and quality control

Hi Michael, we showed that motion (even the one that you cannot really see in the image) produces biased measurements (and not just in FreeSurfer but also other methods). FS handels all kinds of data, even really crappy images, and that is exactly the problem, as these measurements can be seve

Re: [Freesurfer] Head Motion -- was: surface reconstruction and quality control

Hi Martin, I totally agree that we need robust approaches to either correct for motion during the structurals in real time (as you guys have been working on with your vNav sequence), or start at least quantifying motion during structural imaging (e.g,. again by using the same vNav sequence,

Re: [Freesurfer] Head Motion -- was: surface reconstruction and quality control

Yes, I wanted to make those images available, but this was not in the consent forms and I don't think it will be possible to re-consent the subjects. I pushed that a little a while ago, will try again. Martin On 08/05/2015 08:17 PM, Harms, Michael wrote: Hi Martin, I totally agree that we ne

Re: [Freesurfer] Head Motion -- was: surface reconstruction and quality control

I forgot to mention, we used the QC protocol described here: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-investigators/qc with a manual of examples: http://cbs.fas.harvard.edu/usr/mcmains/CBS_MRI_Qualitative_Quality_Control_Manual.pdf where Fig. 6 in our paper sho

Re: [Freesurfer] registering NHP data

There are 2 papers the describe the atlas and method for normalization. (1) McLaren et al. 2009. NeuroImage. A population-average MRI-based atlas collection of the rhesus macaque. (2) McLaren et al. 2010. Methods. Rhesus macaque brain morphometry: A methodological comparison of voxel-wise approache

[Freesurfer] (no subject)

Hi, The recon pipeline outputed an apparently correct file, which happen to confuse freesurfer reading functions. I attached a slightly-altered file named lh.data_crash which have the same problem. The other file named lh.data_nocrash seems to be parsed fine, despite differing by only 1 float-

[Freesurfer] [possible Bug] Unexpected parse error during reading of lh.area

From: zorze...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Date: Thu, 6 Aug 2015 07:42:40 +0200 Hi, The recon pipeline outputed an apparently correct file, which happen to confuse freesurfer reading functions. I attached a slightly-altered file named lh.data_crash which have t