[Freesurfer] FastSurfer with FreeSurfer version 7.1.0?

External Email - Use Caution Dear all, I noticed FastSurfer also seems to run with a 7.1.0 FS version. Or is there any reason not to do this? Thank you, Kind wishes, Barbara ___ Freesurfer mailing list

Re: [Freesurfer] Freeview Scrolling through slices on a Mac

External Email - Use Caution Dear Chris, We're actually working on control points in our group as well - on Mac you have to press the 'fn' (very left bottom key) along with the up-down arrow keys. Hope that helps, Cheers, Barbara On 11/12/2018 18:36, Ruopeng Wang wrote: >

Re: [Freesurfer] TRACULA tract reconstruction

Hi Joëlle, Which scanner was used to acquire the images? I have used Osirix light in the past to anonymize my dicom images, maybe you'd like to try that? Best wishes, Barbara On 29/03/2017 13:30, Joëlle Ismay Rosanne Van Der Molen wrote: ​Hi Anastasia, Yes, I use dicom images as input

Re: [Freesurfer] Unpacking DWI Data

*From:* freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Barbara Kreilkamp <bakk@googlemail.com> *Sent:* Sunday, September 18, 2016 3:21:00 PM *To:* Freesurfer support list *

Re: [Freesurfer] Unpacking DWI Data

Hi Emily, I've never tried to use unpacksdcmdir but you may try the Osirix tool, it allows you to read in a dicom folder and save a new folder with subfolders according to the sequences that were run. At the same time you can also anonymize your data. Does this help? Best wishes,

Re: [Freesurfer] TRACULA tract endpoints on cortical surface

rf-fwhm 6. There are other options in > mri_vol2surf, I'd recommend playing with the settings to see what works > better for your data. > > Best, > > a.y > > > On Fri, 5 Aug 2016, Barbara Kreilkamp wrote: > >> Dear Freesurfers and TRACULA experts, >> &g

[Freesurfer] Fwd: TRACULA tract endpoints on cortical surface

Dear all, If you have some suggestions I'd greatly appreciate them. Thank you very much, Best wishes, Barbara Forwarded Message Subject:TRACULA tract endpoints on cortical surface Date: Fri, 5 Aug 2016 12:03:02 +0200 From: Barbara Kreilkamp <b

[Freesurfer] TRACULA tract endpoints on cortical surface

Dear Freesurfers and TRACULA experts, Thank you for your help so far. I am trying to map the endpoints of the tract probability distributions onto the cortical surface (as mentioned in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos). I've somehow gathered that I need to do this (example

[Freesurfer] flipping TRACULA tracts

Dear Freesurfers, I've got data pertaining to patients with left and right-sided temporal lobe epilepsy (TLE). My aim is to group those tracts according to side of epilepsy for waypoint comparisons. Basically for patients with right TLE I'd like to look at right tracts and at the same time

[Freesurfer] TRACULA fornix tractography

Dear Anastasia, As we are analyzing DTI data acquired in patients with epilepsy we are especially interested in the fornix. I've come across the mri_cc -f option for fornix segmentation (native space) but I've also read that manual tracing/labeling of the tracts would be needed in the 33

Re: [Freesurfer] TRACULA tract group comparison p-values

s that go all the way from negative to > positive (which is what I suspect you have). > > I'll submit this request to freeview headquarters :) Hopefully we can get > it in there quickly. Thanks for your patience! > > a.y > > On Sun, 10 Jul 2016, Barbara Kreilkamp wrote: >

Re: [Freesurfer] TRACULA tract group comparison p-values

you're > trying to display). We should definitely add it in the future. > > Best, > a.y > > On Wed, 6 Jul 2016, Barbara Kreilkamp wrote: > >> Dear Freesurfers, >> >> I am looking for a way to add a colorbar to my p-value tract cores >> generated through TRA

[Freesurfer] Freeview: how to change spline color bar

Dear Freesurfers, How would I be able to use a different colormap under point sets please? I can only find "solid color" and "heatmap" but a blue to red colorbar would suit my needs more. Any assistance is greatly appreciated. Thank you, Best wishes, Barbara

Re: [Freesurfer] question about white matter edits

Hi Rito, I just read this today myself "Select a few control points around your trouble areas, space them out throughout the brain and on different slices. You want to pick points in a region where the wm intensity is lower than it should be (that is, having a voxel value less than 110)."

[Freesurfer] TRACULA tract group comparison p-values

Dear Freesurfers, I am looking for a way to add a colorbar to my p-value tract cores generated through TRACULA. When I load up the images as described in the tutorial here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics I only get a colorbar from 0 to 28.5 which cannot

Re: [Freesurfer] segmentation issues in Temporal Lobes

th the subfield stuff), but we exclude it from our analyses so you should > be fine > > cheers > Bruce > > On Wed, 6 Jul 2016, Barbara Kreilkamp > wrote: > >> Dear Freesurfers, >> >> Unfortunately I am having a problem with recon-all segmentation in some of

[Freesurfer] Fwd: ERROR: mpr2mni305 failed gauss_4dfp mpr2mni305

Forwarded Message Subject:ERROR: mpr2mni305 failed Date: Sat, 28 May 2016 14:27:29 +0200 From: Barbara Kreilkamp <bakk@googlemail.com> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Dear FSL experts, I am running freesurfer-Darwin

[Freesurfer] ERROR: mpr2mni305 failed

Dear FSL experts, I am running freesurfer-Darwin-lion-stable-pub-v5.3.0 on MAC 10.10.5. Could you please help me with this error message? I think it relates to the library, this is what it states in talairach_avi.log. But I am unsure how to solve this issue. Any help is greatly appreciated,

[Freesurfer] hippo subfield segmentation new beta version (version 6)

Dear all, Would you please help me on this one? Thank you, best wishes, Barbara Forwarded Message Subject:hippo subfield segmentation new beta version (version 6) Date: Wed, 20 Apr 2016 11:45:02 +0100 From: Barbara Kreilkamp <bakk@gmail.com> To: Free

[Freesurfer] hippo subfield segmentation new beta version (version 6)

Dear all, I've been reading the manuscript on version 6 freesurfer hippocampal subfield segmentation "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: application to adaptive segmentation of in vivo MRI" Can you please tell me if the type of

Re: [Freesurfer] Freesurfer version 6.0

t; is using the 6.0-beta version > released several months ago, which has been significantly modified since > its beta release. > > -Zeke > > On 02/17/2016 11:45 AM, Barbara Kreilkamp wrote: >> Dear all, >> >> Sorry to bother you again. I am a bit confused as

Re: [Freesurfer] Freesurfer version 6.0

this link from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/ but it does not seem to point anywhere anymore. Thank you very much, Barbara On 17/02/2016 14:30, Barbara Kreilkamp wrote: > Dear Douglas, > > Thanks a lot, I found the version. > Best wishes, > Ba

Re: [Freesurfer] Freesurfer version 6.0

; > On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote: >> Dear Freesurfer experts, >> >> How may I get Freesurfer v 6 ? >> >> Thank you very much, >> Best wishes, >> Barbara >> ___ >&g

[Freesurfer] Freesurfer version 6.0

Dear Freesurfer experts, How may I get Freesurfer v 6 ? Thank you very much, Best wishes, Barbara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail

[Freesurfer] PhD position: MRI markers of neuroinflammation in treatment pharmacoresistant epilepsy

all details about this position via this link: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=70289=3417 *Deadline:* Friday, January 22, 2016 - apply ASAP! Best wishes and a Happy New Year! Barbara Kreilkamp PhD researcher University of Liverpool

Re: [Freesurfer] SNR Tracula

Hi Scott, This previous post might help you. https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41439.html Best wishes, Barbara On Sun, Nov 8, 2015 at 10:43 PM, Scott Quadrelli wrote: > Hi, > > Tracula outputs the SNR for each volume in a txt file. I was

Re: [Freesurfer] TRACULA and eddy (FSL)

, and turn off the default eddy correction (then it won't rotate anything, either). I'll probably make it an option in the upcoming version to use eddy. Best, a.y On Tue, 25 Aug 2015, Barbara Kreilkamp wrote: Dear TRACULA experts and developers, I am wondering whether TRACULA will allow

[Freesurfer] TRACULA and eddy (FSL)

Dear TRACULA experts and developers, I am wondering whether TRACULA will allow usage of eddy, the newer eddy-correction tool from FSL in a newer version? Alternatively, it seems it would be possible to use the eddy corrected nifti plus bvec and bval as the original input to TRACULA and turn

Re: [Freesurfer] Using TRACULA ROI for image in diffusionspace

space). To be consistent with the FA, MD, etc stats that are produced by default by trac-all, you'd threshold path.pd.nii.gz to 20% of its max value before using it as an ROI. Hope this helps, a.y On Mon, 16 Feb 2015, Barbara Kreilkamp wrote: Dear TRACULA experts, I wonder if you could

Re: [Freesurfer] Using TRACULA ROI for image in diffusionspace

high value it won't take them into account, which is probably a good idea here). Then use 20% of that robust maximum as your lower threshold and voila, you have your ROI. Best, a.y On Wed, 18 Feb 2015, Barbara Kreilkamp wrote: Thank you very much Anastasia, May I please check with you

[Freesurfer] Using TRACULA ROI for image in diffusionspace

Dear TRACULA experts, I wonder if you could please assist me in extracting tract values from an image I transferred to diffusion space. I ran TRACULA on my DTI dataset, however from other structural images I aim to extract values for tracts as well. I also extracted DTI derived measures from

Re: [Freesurfer] TRACULA dwi flipping

Thank you Anastasia. Best wishes, Barbara On 21/11/2014 21:45, Anastasia Yendiki wrote: Hi Barbara - It's converting to LAS orientation. If it the images are already in LAS orientation, that command will have no effect, as you say. a.y On Fri, 17 Oct 2014, Barbara Kreilkamp wrote: Dear

[Freesurfer] TRACULA dwi flipping

Dear all, Would you please explain why TRACULA is flipping the data so often? And what does the flip4fsl command do? The data I have is already in the right (radiological) orientation. fslswapdim does not seem to have an effect either, as the parameters are just set to 'x y z'. Are these

[Freesurfer] TRACULA preprocessing: bvector rotation, negative eigenvalues

Dear all, Do you have suggestions/ideas for me please? Thank you, Barbara Original Message Subject:TRACULA preprocessing: bvector rotation, negative eigenvalues Date: Tue, 07 Oct 2014 19:09:00 +0100 From: Barbara Kreilkamp bakk@gmail.com To: Freesurfer

[Freesurfer] TRACULA preprocessing: bvector rotation, negative eigenvalues

Dear Freesurfers, I am looking for information on how exactly the b-table gets rotated. 1. It seems that eddy_correct runs once with 12 doF, and then the bmatrix gets updated based on this registration. Would you please confirm? 2. I know that my data has negative eigenvalues (most of them

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

is still a dot (see screenshot of the brain view from the bottom). Any further suggestion? Thanks. [image: Inline image 2] On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari cavallari.mich...@gmail.com wrote: Thanks! it's running... On Thu, Sep 11, 2014 at 1:31 PM, Barbara

[Freesurfer] bbregister with T2 in trac-preproc

Dear Freesurfers, I would like to alter the trac-preproc to include an EPI to T2 registration (diffeomorphic) as I do not have a field map, is there a way of doing this? I saw that bbregister actually only uses 6 doF. Thank you very much, Barbara ___

[Freesurfer] trac-all: saving tensor in dtifit

Dear all, I would like to make amendments to the FSL dtifit call during trac-preproc. In which way can I edit the call in trac-preproc? # LS tensor estimation set cmd = dtifit set cmd = ($cmd -k $dwidir/dwi.nii.gz) set cmd = ($cmd -m $brainmask) set cmd = ($cmd -r $dwidir/bvecs) set

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

Hi Michele, Don't think there is anything wrong with the attached dmrirc.tutorial file. You definitely need to add the '-c' flag infront of the path to your configuration file. Right now it reads the path to your file as a flag, which is of course not what you want. Best, Barbara On

[Freesurfer] freesurfer commands from MATLAB

Dear Freesurfers, Is there a way of calling freesurfer-scripts from within MATLAB? I know there are some setups needed to make MATLAB understand where it can find the commands (I have done this before with FSL). I am using bash, and when I type the Freesurfer commands in a terminal by hand, they

Re: [Freesurfer] freesurfer commands from MATLAB

. system('mycommand') .) Best, Markus 2014-09-09 13:45 GMT+02:00 Barbara Kreilkamp bakk@googlemail.com: Dear Freesurfers, Is there a way of calling freesurfer-scripts from within MATLAB? I know there are some setups needed to make MATLAB understand where it can find the commands (I have done

Re: [Freesurfer] tracula: bvec-error

Hi Robby, Thanks for sharing this and making me aware of the update (great that this one will give you the motion parameters as well!). So also for me it works now! Have fun with your tracts of many subjects then :)! Barbara On 05/09/2014 09:22, Robby De Pauw wrote: Hi Anastasia and Barbara

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

tracula pre-processing (with errors) and recon-all (apparently without errors). Any help/suggestions? Thanks. On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com wrote: Hi Michele, This might be the solution - try the command 'more

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

help/suggestions? Thanks. On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com wrote: Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

the very same dicoms and bval/bvec. Any suggestion? Thanks On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

-0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025 You are ending up with multiple columns in the second row, please make sure they are 3 columns. Good luck, Barbara On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele

Re: [Freesurfer] tracula: bvec-error

Dear all, Robby, are you still having the problem? Did you solve it? I am really having the same problem, just that I am using nifti files instead of dicoms. I am using the same version as Robby. Please find my command+output, trac-all.log and configuration file in the attachment. I would also

Re: [Freesurfer] tracula: bvec-error

, Barbara Kreilkamp bakk@googlemail.com mailto:bakk@googlemail.com wrote: Dear all, Robby, are you still having the problem? Did you solve it? I am really having the same problem, just that I am using nifti files instead of dicoms. I am using the same version as Robby. Please find my

Re: [Freesurfer] recon-all normalization: bias field output

like to be sure. Thank you very much, Barbara On Thu, Aug 28, 2014 at 3:27 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Dear Bruce and Christian, I found the easy way of simply writing 'set cleanup = 0' at the beginning of mri_nu_correct.mni and then I run this command

Re: [Freesurfer] recon-all normalization: bias field output

hold of the low-intensity voxel mask that N3 operates within. You can use this to constrain the division mentioned in 1). Best, Christian On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote: Dear all, Is there a way to output the N3's (non-parametric normalization step) output? I am interested

Re: [Freesurfer] recon-all normalization: bias field output

the exact inputs and outputs of nu_correct. cheers Bruce On Thu, 28 Aug 2014, Barbara Kreilkamp wrote: Dear Christian, Thanks a bunch for this answer. I ran all the steps you mentioned (except for the one where I simply do uncorrected/corrected, as these images have different dimensions

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On

[Freesurfer] recon-all normalization: bias field output

Dear all, Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities. Thank you for your help, Barbara ___ Freesurfer mailing list

[Freesurfer] trac-all bvec (nifti many subjects)

Dear Freesurfers, I am trying to run trac-all with many subjects through a configuration file. The first subject gets processed without error, but after that I keep getting errors, that the dwi_orig_flip.mghdti.bvecs file cannot be found. This is my command with the output (below configuration