[Freesurfer] Extract single time frame

2015-10-26 Thread Rockers, Elijah D.
Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify

Re: [Freesurfer] Extract single time frame

2015-10-26 Thread Rockers, Elijah D.
Alternatively, all of our tools accept the extension # so you could do: mri_convert file.nii#5 file.frame5.nii cheers Bruce On Mon, 26 Oct 2015, Rockers, Elijah D. wrote: Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I

[Freesurfer] Exporting ROIs as .nii

2015-10-05 Thread Rockers, Elijah D.
Hello, We are interested in finding a way to use particular parcellations from Freesurfer in a separate program. For instance, we are very happy with the way Freesurfer parcellates the Choroid Plexus and separates the Cerebellum into white and gray matter regions, and would like to import

[Freesurfer] voxel value scaling

2015-11-25 Thread Rockers, Elijah D.
I am interested in finding a way to apply a slope scaling factor to the voxel values in a NIfTI image. I have done this in MATLAB and PMOD so far, but for some reason both methods change the origin or otherwise distort the dimensions of the image and render it impossible for me to process

Re: [Freesurfer] voxel value scaling

2015-11-25 Thread Rockers, Elijah D.
Great thank you! On 11/25/2015 11:54 AM, Douglas Greve wrote: > You can use fscalc, something like > fscalc input.nii mul 10 -o output.nii > I think you can use fslmaths as well > > On 11/25/15 12:08 PM, Rockers, Elijah D. wrote: >> I am interested in finding a way to

[Freesurfer] recon-all warnings

2016-06-23 Thread Rockers, Elijah D.
Hello, Doing a recon-all -all yields some deprecation warnings. defined(@array) is deprecated at /freesurfer/mni/bin/nu_estimate_np_and_em line 165. Use of ?PATTERN? without explicit operator is deprecated at /freesurfer/mni/bin/sharpen_volume line 153. I think my results should still be OK

[Freesurfer] XNAT Freesurfer custom datatype

2016-03-23 Thread Rockers, Elijah D.
Trying to integrate freesurfer data with our XNAT database. Are there any freesurfer schemas for XNAT available, or is it pretty much I have to try to make my own? Thanks, -- Elijah Rockers Research Data Analyst Houston Methodist Neurological Institute O: 713 363 7729 Houston Methodist.

[Freesurfer] HIRING: Research Assistant

2016-03-19 Thread Rockers, Elijah D.
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

[Freesurfer] Hiring: Houston, TX - Data Processing/Analysis

2016-03-07 Thread Rockers, Elijah D.
Hello, The Nantz National Alzheimer Center, in Houston, TX is looking to fill two positions pertaining to neuroimaging and analysis. Be aware that we cannot accept remote employment, the candidate would have to work day-to-day in the city of Houston. Any interested person is encouraged to

[Freesurfer] X graphics issues via SSH

2016-05-11 Thread Rockers, Elijah D.
Hello freesurfers, Running a Mac Pro, OS X El Capitan 10.11.4 With ATI Radeon Graphics card, and XQuartz v 2.7.9 I am able to run Qdec and freeview perfectly fine on my machine. The problem comes when I attempt to SSH into another machine and use these programs (it used to work fine, but I am

Re: [Freesurfer] X graphics issues via SSH

2016-05-12 Thread Rockers, Elijah D.
After much scouring, this appears to be a problem with XQuartz. I spoke to someone on the XQuartz team and they are basically on life-support. It looks like support for this may be going down the toilet, and migration to an entirely new architecture is needed. I am not the only person

[Freesurfer] Disastrous Soft Error

2017-02-24 Thread Rockers, Elijah D.
Hello all, I recon-all'd ~40 different subjects. I have been going through all the images to make sure they were processed correctly. Most required no no editing and recon-all did a very good job. But for one scan in particular, it looks like Freesurfer thinks the top of the spinal cord is the

Re: [Freesurfer] Disastrous Soft Error

2017-02-24 Thread Rockers, Elijah D.
As far as I can tell, everything looks OK up until brainmask.mgz. The skullstrip step seems to have cropped out the brain and left the neck... On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote: > Hello all, > > I recon-all'd ~40 different subjects. I have been going through all the >

Re: [Freesurfer] Disastrous Soft Error

2017-02-24 Thread Rockers, Elijah D.
OK, sorry for spamming the list. I fixed the the faulty skullstrip by using recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid Currently redoing the surface reconstructions, but it should be OK now. Thanks for the nice documentation. Eli On Fri, 2017-02-24 at 15:30 -0600, Elijah Rockers

Re: [Freesurfer] No FTP Access

2017-02-22 Thread Rockers, Elijah D.
Nevermind. I discovered if I just change ftp to https in the download link, it works fine. - Eli On Wed, 2017-02-22 at 12:22 -0500, Elijah Rockers wrote: > Is there by any chance another way to download Freesurfer? My > institution does not allow FTP connections (HIPPA...) Same goes for the >

[Freesurfer] No FTP Access

2017-02-22 Thread Rockers, Elijah D.
Is there by any chance another way to download Freesurfer? My institution does not allow FTP connections (HIPPA...) Same goes for the tutorial data, but obviously Freesurfer is the priority here... thanks. - Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized

[Freesurfer] Freeview default cursor

2017-02-28 Thread Rockers, Elijah D.
Hello, I could not find any information on changing the cursor via command line. My goal is to persistently change the default cursor style/color, I was going to create an alias on my system. Thanks, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston

Re: [Freesurfer] Manual edit to include missing cortex?

2017-03-01 Thread Rockers, Elijah D.
the list at > freesurfer-ow...@nmr.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. Manual edit to include missing cortex? (Rockers, Elijah D.) >

[Freesurfer] Manual edit to include missing cortex?

2017-02-27 Thread Rockers, Elijah D.
Is there something I can do to extend the pial surface to include cortex that it ignored? In some places there are rather large chunks of cortex not included in the pial surface. http://imgur.com/a/FnAgj Link is to a screenshot, notice the top of the brain. It's fairly pronounced, visible in 12

[Freesurfer] mri_convert slope scale

2016-11-09 Thread Rockers, Elijah D.
Hello, We have been using mri_convert to convert our dicoms into .nii niftis. There is an entry in the .nii header for the slope scale, but mri_convert appears to discard this value instead of copying it into the header (whereas mricron retains this value) We prefer to use mri_convert. Is

Re: [Freesurfer] mri_convert slope scale

2016-11-10 Thread Rockers, Elijah D.
think we > actually apply the scaling, so including it in the output would be > inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote: >> >Hello, >> > >> >We have been using mri_convert to convert our dicoms into .nii niftis. >> >There is an entr

Re: [Freesurfer] mri_convert slope scale

2016-11-10 Thread Rockers, Elijah D.
(eg Freeview..) to apply the scaling.. Hope this clarifies. Thanks for checking into this. On 11/10/2016 12:18 PM, Douglas N Greve wrote: > Sorry, is it a scale in the dicom file or the nifti file that is not > being applied properly? > > > On 11/10/2016 11:01 AM, Rockers,

Re: [Freesurfer] mri_convert slope scale

2016-11-10 Thread Rockers, Elijah D.
gt; On 11/10/2016 01:29 PM, Rockers, Elijah D. wrote: >> As far as I can tell, mri_convert doesn't apply the scaling factor, and >> also doesn't copy over the slope scale header entry, when converting >> from dicom to nifti. >> >> By contrast, dcm2nii does not apply th

[Freesurfer] S. Nigra

2016-10-17 Thread Rockers, Elijah D.
Is it possible for freesurfer to parcellate the substantia nigra from a T1? -- Elijah Rockers Research Data Analyst Houston Methodist Research Institute O: 713-363-7729 Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20

Re: [Freesurfer] mri_convert slope scale

2016-11-18 Thread Rockers, Elijah D.
ing the PET after setting this env var > > setenv FS_SLICE_LIN_SCALE 1 > > This causes mri_convert to read 28,1052 (intercept) and 28,1053 > (slope). the output value should be > > dicomvalue*slope + intercept > > Is 2005,100e accompanied by an intercept ? > > > >

Re: [Freesurfer] mri_convert slope scale

2016-11-18 Thread Rockers, Elijah D.
t; > On 11/10/2016 12:40 PM, Douglas N Greve wrote: >> What is the dicom tag for the scale? >> >> >> On 11/10/2016 01:29 PM, Rockers, Elijah D. wrote: >>> As far as I can tell, mri_convert doesn't apply the scaling factor, and >>> also doesn't copy ov

[Freesurfer] white matter disease

2017-03-27 Thread Rockers, Elijah D.
Hello, We have a large number of subjects processed with the default settings of recon-all. Unfortunately the presence of white matter creates problems when creating the white matter surface. There are large hypo-intensities in the white matter which badly distort the surfaces in multiple

[Freesurfer] wm.mgz manual editing, revisited

2017-03-07 Thread Rockers, Elijah D.
Hello all, Again, I tried to modify the white matter surface by adding voxels to the wm.mgz file, and performed the reconstruction by doing the following. -Opened brainmask.mgz for reference -Opened wm.mgz on top of that -Click the voxel edit button -Check the recon editing checkbox -Fill in

Re: [Freesurfer] wm.mgz manual editing

2017-03-02 Thread Rockers, Elijah D.
are talking about? > > Also, in general it is hard for us to help you unless you include more > information. What exact command did you run? What was the screen output? > What was in the recon-all.log? > > cheers > Bruce > > > On Wed, 1 > Mar 2017, Rockers, El

[Freesurfer] wm.mgz manual editing

2017-03-01 Thread Rockers, Elijah D.
Couple of questions: 1) I edited wm.mgz following the instructions in the wiki guide, but it did not change anything after reconstruction. I am still using 5.3 right now, so maybe the guide is wrong for me. What is the brush value supposed to be? I used 255 but it did not extend the white matter

Re: [Freesurfer] wm.mgz manual editing

2017-03-02 Thread Rockers, Elijah D.
are talking about? > > Also, in general it is hard for us to help you unless you include more > information. What exact command did you run? What was the screen output? > What was in the recon-all.log? > > cheers > Bruce > > > On Wed, 1 > Mar 2017, Rockers, El

[Freesurfer] mri_surf2vol

2017-08-10 Thread Rockers, Elijah D.
I am attempting to create a volume from a surface. My ultimate goal is to obtain a mask that includes everything "inside" the white matter surfaces. wm.mgz is close, but it would nicer to just get a mask from lh.white and rh.white. I would like these masks to be in the subject's native space.

[Freesurfer] Segmentation of WM hypointensities

2017-08-16 Thread Rockers, Elijah D.
Hello, The Freesurfer segmentation for hypointensities is very good, but misses on some subjects, i.e. it does not include large chunks of hypointense regions in some subjects. It does fantastic picking up the periventricular hypointensities, but appears to fail on some deep WM regions. I just

[Freesurfer] mri_glmfit --cortex flag

2017-07-27 Thread Rockers, Elijah D.
From what I understand, the --cortex flag is simply supposed to zero out any signal in the medial wall with a mask, I checked mask.mgh, it is 0 on the medial wall and 1 everywhere else as expected... however when I analyze the data without this flag, the resulting sig.mgh file has completely

[Freesurfer] Qdec input fields

2017-06-28 Thread Rockers, Elijah D.
Hi, We like using Qdec to display cortical thickness results. The only drawback is that we are unable to manually input values into the boxes for threshold values, FDR rate, etc.. We are running Centos7. We thought the graphics drivers were the problem, but even after buying a whole new GFX

[Freesurfer] Monte Carlo error (fwhm4 vs. fwhm04)

2017-06-01 Thread Rockers, Elijah D.
Hello FS, I am attempting to run a monte carlo simulation on some cortical thickness data in Qdec 1.5, but I get the following error: ERROR: CSDread(): could not open ../freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm4/abs/th40/mc-z.csd I thought it might be a permissions issue

Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6)

2017-08-23 Thread Rockers, Elijah D.
mory. > On Aug 23, 2017, at 11:21 AM, Rockers, Elijah D. > <edrock...@houstonmethodist.org<mailto:edrock...@houstonmethodist.org>> wrote: > > We encountered a hard failure, below is the tail of the log. We are currently > running Freesurfer 6 again locally to see if it suc

[Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6)

2017-08-23 Thread Rockers, Elijah D.
We encountered a hard failure, below is the tail of the log. We are currently running Freesurfer 6 again locally to see if it succeeds on a desktop machine (this is the first time encountering a hard failure on the XNAT server). Any suggestions? -merging segment 180 into 178 160 defects

[Freesurfer] Cortical thickness clarification

2017-12-12 Thread Rockers, Elijah D.
Hello, I was hoping to get some clarification on how exactly the cortical thickness number is calculated. In the videos, Doug says it's "the distance between the vertex on the white to the vertex on the pial, and you go backwards and forwards to compute the average thickness", and the 2000

Re: [Freesurfer] reconstruction for very significant atrophy

2018-01-11 Thread Rockers, Elijah D.
check to make sure everything is lining up correctly? - Eli On Thu, 2018-01-11 at 08:08 -0500, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 5 Date: Wed, 10 Jan 2018 20:26:11 + From: "Rockers, Elijah D." <edrock...@houstonmethodist.org<mailto:edrock...@hous

Re: [Freesurfer] reconstruction for very significant atrophy

2018-01-11 Thread Rockers, Elijah D.
32...@gate.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" do you mean that the entire surface is off by a fixed amount? On Thu, 11 Jan 2018, Rockers, Elijah D. wrote: Thanks Bruce. I went over some more images with our PI and he was mostly satisfied with the p

[Freesurfer] reconstruction for very significant atrophy

2018-01-10 Thread Rockers, Elijah D.
Hello, We have some images that reflect severe atrophy in some subjects, in which gray matter is virtually undetectable on the MRI in some regions. However, upon checking the segmentations visually, the white/pial surfaces are reflecting a significant cortical thickness in these areas. Is

[Freesurfer] mri_convert trying to find DWI parameters from Philips scans

2018-01-24 Thread Rockers, Elijah D.
Hello, I am using mri_convert to convert my standard T1-weighted structural images into nifti format. The conversion works, but it might be somewhat delayed due to spamming the console with the following message ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR:

[Freesurfer] Surface editing: recon-all exited with errors

2018-07-30 Thread Rockers, Elijah D.
External Email - Use Caution Hello. I manually edited the brainmask.mgz file for three subjects. This was done to prevent the pial surface from extending into non-cortical areas, in particular the soft-tissue near the brain stem, and some cerebellar areas. Usually this type

Re: [Freesurfer] Surface editing: recon-all exited with errors

2018-07-31 Thread Rockers, Elijah D.
31, 2018 2:14:18 PM To: Freesurfer support list Cc: Rockers, Elijah D. Subject: Re: [Freesurfer] Surface editing: recon-all exited with errors h, maybe -make all has changed (or my memory of what it does is incorrect). I'll find someone else here to help you out cheers Bruce On Tue, 31 Jul 2018, Bruce Fisc

Re: [Freesurfer] Surface editing: recon-all exited with errors

2018-08-01 Thread Rockers, Elijah D.
External Email - Use Caution Hi Andrew, Looks like that cleared the errors. Thank you both, -Eli From: Hoopes, Andrew Sent: Tuesday, July 31, 2018 3:09 PM To: Freesurfer support list Cc: Rockers, Elijah D. Subject: Re: [Freesurfer] Surface

[Freesurfer] surface arithmetic?

2018-08-07 Thread Rockers, Elijah D.
External Email - Use Caution Hello, I have a subject with two MRIs and surface reconstructions, several years apart. I would like to directly compare these surfaces if possible, for instance, to subtract (new - old) to see a "difference surface" or something similar. Is there

[Freesurfer] T1 / T2 WMH Segmentation

2018-03-16 Thread Rockers, Elijah D.
Hello, I noticed that recon-all automatically segments hypointesities in the white matter regions. Is there any possibility of using Freesurfer to segment T2 FLAIR WMH? I did not see anything in the Wiki documentation about it. Thanks, - Eli Houston Methodist. Leading Medicine. Houston

[Freesurfer] T1 hypointensities

2019-01-07 Thread Rockers, Elijah D.
External Email - Use Caution Hello, Are the WM-hypointensities segmented in the same way as the rest of the subcortical regions? i.e., using the probablistic atlas referenced in the 2002 Fischl et al paper? Thanks, - Eli Houston Methodist. Leading Medicine. Houston

[Freesurfer] freeview command line options

2019-09-20 Thread Rockers, Elijah D.
External Email - Use Caution Hello, it's possible I found a bug in freeview: I'm using the overlay_color option with freeview. Specifically I am trying to use both the "truncate" and "inverse" options in a command line call to freeview for a pipeline I am building. The

[Freesurfer] mri_glmfit: don't display "positive"

2019-09-20 Thread Rockers, Elijah D.
External Email - Use Caution Hello, with Qdec, there was an option to "remove" positive (or negative) results from the displayed overlay... Is it possible to do something similar with the results of mri_glmfit, but displaying with freeview instead? For instance, if I wanted

[Freesurfer] qdec / tksurfer GUI

2020-02-07 Thread Rockers, Elijah D.
External Email - Use Caution I've noticed an issue when trying to manually input values into fields with Qdec. This problem has been reported before. I thought perhaps it was because Qdec is deprecated, so I loaded the results into tksurfer, and I can't change fields in this

[Freesurfer] White matter hypointensities

2020-04-03 Thread Rockers, Elijah D.
External Email - Use Caution Hello, When was the wm-hypointeisities label added to the Freesurfer segmentation? Is there any paper that explicitly mentions this, or should I just cite the 2002 paper? Thanks, -Eli Houston Methodist. Leading Medicine. Houston Methodist is