Re: [Freesurfer] mri_nu_correct.mni and mri_convert with odd matrix dimensions and "-cm" flag

2015-02-10 Thread Falk Lüsebrink
Hi Natalia, I had the same issue in some cases. This is happens if you native data is not perfectly isotropic and seems to be related to a rounding error. The only the solution I found is to fix the resolution of your data prior to mri_nu_correct manually. Check your voxel size with mri_info.

Re: [Freesurfer] freesurfer pipeline for sub mm voxel resolution

2015-04-08 Thread Falk Lüsebrink
Hi Ri, you can process data with higher resolution than 1mm^3 if you follow the HiResRecon (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). The changes to the pipeline were done using v5.1, however, this should still work fine. Best, Falk -Ursprüngliche Nachricht- Von: freesurfe

Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

2015-06-25 Thread Falk Lüsebrink
: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data Hello! I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki

Re: [Freesurfer] correction for field dishomogeneity

2015-07-06 Thread Falk Lüsebrink
Hi Clelia, I think the reviewer might refer to the -3T flag of recon-all which enables 3T-specific NU intensity correction parameters and usage of a special atlas for Talairach alignment. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im

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

2015-08-11 Thread Falk Lüsebrink
Me too. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Andrea Grant Gesendet: Montag, 10. August 2015 16:23 An: Freesurfer support list Cc: Kyoko Fujimoto; Jonathan Polimeni Betreff: Re: [Freesurfer] options for 7T images...

Re: [Freesurfer] Freesurfer program for 7 Tesla

2016-06-08 Thread Falk Lüsebrink
Hi Prasad, for me FreeSurfer worked pretty nicely with 7T data. Most critical parts are skull-stripping and surface alignment if intensities of the cortex vary a lot (e.g. darker cortex in temporal lobes). However, I haven’t tried the hippocampal subfields yet and have usually processed small c

[Freesurfer] mri_ca_label with high resolution data

2016-07-18 Thread Falk Lüsebrink
ew minutes on 1 mm data only? Would it help to add the openmp flag in that case? Best, Falk ---- Falk Lüsebrink, M. Sc. Otto-von-Guericke-Universität Magdeburg Forschungscampus STIMULATE http://www.forschungscampus-stimulate.de/ Universitätsplatz 2 39106 Magde

Re: [Freesurfer] mri_ca_label with high resolution data

2016-07-19 Thread Falk Lüsebrink
ischl Gesendet: Dienstag, 19. Juli 2016 15:37 An: Freesurfer support list Betreff: Re: [Freesurfer] mri_ca_label with high resolution data Hi Falk I think openmp will help with this in V6, but probably not before Bruce On Tue, 19 Jul 2016, Falk Lüsebrink wrote: > > Hi all, > >   &

Re: [Freesurfer] question about voxel size

2016-07-19 Thread Falk Lüsebrink
Hi Dorsa, until version 6 of FreeSurfer is released you could try to follow the HiResRecon (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon) which should enable you to process the data in its native resolution. With FreeSurfer v6 this workaround will not be necessary anymore, as the proces

Re: [Freesurfer] question about voxel size

2016-07-19 Thread Falk Lüsebrink
can jump in on that. Best, Falk P.S. Be sure to also reply to the list also. Von: Dorsa Haji Ghaffari [mailto:gh...@umich.edu] Gesendet: Dienstag, 19. Juli 2016 18:21 An: Falk Lüsebrink Betreff: Re: [Freesurfer] question about voxel size Thank you. I was actually able to get results using my high

Re: [Freesurfer] mri_ca_label with high resolution data

2016-07-21 Thread Falk Lüsebrink
9 Jul 2016, Falk Lüsebrink wrote: > > Hi all, > >   > > I’m currently processing a 250 µm MPRAGE with a dev build from mid of May. > Running recon-all with default parameters ran flawlessly. Afterwards I > added the -hires flag to process the data without conformatio

Re: [Freesurfer] mri_ca_label with high resolution data

2016-07-21 Thread Falk Lüsebrink
0 An: Falk Lüsebrink Cc: Freesurfer support list Betreff: Re: AW: [Freesurfer] mri_ca_label with high resolution data Hi Falk the dev version of mri_ca_label does use openmp, so should be faster. cheers Bruce On Thu, 21 Jul 2016, Falk Lüsebrink wrote: > Hi Bruce, > > I started the proces

Re: [Freesurfer] mri_ca_label with high resolution data

2016-07-21 Thread Falk Lüsebrink
Hi Bruce, I thought so. Are there any other means to accelerate this procedure (in the future)? Best, Falk -Ursprüngliche Nachricht- Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 21. Juli 2016 15:52 An: Falk Lüsebrink Cc: Freesurfer support list Betreff

Re: [Freesurfer] mri_ca_label with high resolution data

2016-07-26 Thread Falk Lüsebrink
Hi Bruce, thanks. Keep up the fantastic work! Best, Falk -Ursprüngliche Nachricht- Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 21. Juli 2016 16:44 An: Falk Lüsebrink Cc: Freesurfer support list Betreff: Re: AW: AW: AW: [Freesurfer] mri_ca_label with high

Re: [Freesurfer] Recon hires 7T {Disarmed}

2016-09-21 Thread Falk Lüsebrink
Hi Theresa, first, if you use the -hires flag in version 5.3 the processing pipeline will not start to downsample your data at some point (if I remember correctly during the normalization stage). As you stated that you were expecting the automatic downsampling you should either omit the hires f

Re: [Freesurfer] Processing 7T data

2016-10-06 Thread Falk Lüsebrink
Hi Damien, depending on what you want to do you are forced to use the stable release. The developmental version of FreeSurfer should be used for testing only, not publishing results. Following the notes of the HiResRecon (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon) you should be able

Re: [Freesurfer] [Dev Build] Processing very high resolution dataset

2016-10-12 Thread Falk Lüsebrink
...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Falk Lüsebrink Gesendet: Donnerstag, 6. Oktober 2016 17:51 An: Freesurfer support list Betreff: [Freesurfer] [Dev Build] Processing very high resolution dataset Dear all, I am cur

Re: [Freesurfer] high resolution data using recon-all

2015-10-12 Thread Falk Lüsebrink
Hi Yun, if it is for some reason impractical to use a beta version of FreeSurfer you can also try to follow the HiResRecon (http://freesurfer.net/fswiki/HiResRecon) I put together some time ago. This solves the issues related to high resolution data and will circumvent conformation to 1 mm^3.

Re: [Freesurfer] high resolution data using recon-all

2015-10-12 Thread Falk Lüsebrink
- Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary. On Mon, Oct 12

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

2015-11-30 Thread Falk Lüsebrink
Hi Ajay, I ran into the same error processing hires data a while ago using a nightly build of centos 6 with the hires flag only. Disk space or alike wasn't an issue. I ran mris_topo_fixer instead of mris_fix_topology to get working surfaces. Best, Falk -Ursprüngliche Nachricht- Von: f

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

2015-12-01 Thread Falk Lüsebrink
-qsphere stage again also. Best, Falk Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com] Gesendet: Montag, 30. November 2015 21:50 An: Falk Lüsebrink Cc: Freesurfer support list; Bruce Fischl Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm

Re: [Freesurfer] Replacing / turning off denoising filter

2016-03-19 Thread Falk Lüsebrink
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 publicatio

Re: [Freesurfer] temporal lobe pial surface problem

2016-04-19 Thread Falk Lüsebrink
Hi Xiaomin, currently I don't have access to my notes, however, if I remember correctly, you can specify thresholds in mris_make_surfaces for consideration in the surface placement. This obviously works well only if the contrast between WM/GM/CSF is high enough. If you are interested and nobod

Re: [Freesurfer] recon-all on 0.5mm scan?

2016-05-26 Thread Falk Lüsebrink
Hi Trisanna, you can find instructions on how to process data with an isotropic resolution other than 1mm^3 with FreeSurfer v5.1 and above here: https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon For v5.3 the pipeline should be slightly adapted, however, can easily be done. If you need assist

[Freesurfer] Two questions regarding mri_fill and mris_fix_topology

2013-03-22 Thread Falk Lüsebrink
Dear FreeSurfers,   I am processing some T1-weighted images of the human brain with an isotropic resolution of .5 mm using version 5.1.   After mri_fill my hemispheres are separated nicely and the cerebellum is completely removed. However, looking at the filled.mgz, posterior and superior of th

[Freesurfer] Speeding up mris_fix_topology

2013-01-16 Thread Falk Lüsebrink
Hello all, I'm processing some high resolution data with an isotropic resolution of 0.5mm and I was wondering if it would be possible to speed up mris_fix_topology somehow. Due to the increased number of vertices and also increased number of defects this stage takes incredibly long (e.g. lots o

Re: [Freesurfer] Speeding up mris_fix_topology

2013-01-16 Thread Falk Lüsebrink
Hi Bruce, so you use the conformed and fixed ?h.orig during mris_make_surfaces on the .5mm data? Never thought of that. Best, Falk Original-Nachricht > Datum: Wed, 16 Jan 2013 11:16:45 -0500 (EST) > Von: Bruce Fischl > An: "Falk Lüsebrink"

Re: [Freesurfer] beta

2013-01-22 Thread Falk Lüsebrink
Hi Colin, actually there is no hard limit for the size of your input data, except for the subcortical segmentation which behaves quite strange. What I currently do is to run recon-all on the hires data normally conforming the data. Then I use the upsampled brainmask as a mask to skullstrip my h

Re: [Freesurfer] Expert file for recon-all -hires

2017-02-09 Thread Falk Lüsebrink
Dear Chris and Antonin, I found in some archived message or in the wiki that the default used to be 50 iterations at some time in previous releases of FreeSurfer for standard recon-all. Therefore, I changed it to 50 as default for every resolution in the recent release. This works fine for exam

Re: [Freesurfer] FS v6.0 recon-all freezes

2017-03-10 Thread Falk Lüsebrink
Dear Andrius, You can load the ?h.inflated.nofix in freeview and the overlay ?h.defect_labels to see what's going on. It may be that a chunk of skull or the cerebellum is still attached, in which case you'll want to correct the brainmask.mgz or wm.mgz, respectively, to remove the non-brain tiss

Re: [Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura

2017-05-19 Thread Falk Lüsebrink
Hi Karteek, as for higher resolution (>0.7mm) the brainmask often includes lots of residual, I changed my pre-processing slightly. Currently I do bias field correct my 7T data with SPM and create a mask of the WM, GM and CSF segmentation you get along with it. Then I recon-all -autorecon1 the

Re: [Freesurfer] FreeSurfer on Windows 10 64-bit

2017-07-12 Thread Falk Lüsebrink
Dear Peter, I haven't tried myself, but have a look at: https://github.com/stnava/ANTsR/wiki/Installing-ANTsR-in-Windows-10-(along-with-FSL,-Rstudio,-Freesurfer,-etc). It gives an overview of several neuroscientific tools to be installed using the Windows 10 bash. Best, Falk Von: freesurfer-

Re: [Freesurfer] Switch FreeSurfer Desikan-Killiany atlas to Civet

2017-07-19 Thread Falk Lüsebrink
Dear Antonin, I haven’t used CIVET myself, however, if I remember correctly it employs several metrics to estimate cortical thickness, referred to “Link”, “Laplace”, and “Average Near”. The latter one is a re-implementation of the one used in FreeSurfer. They are described and compared here: h

Re: [Freesurfer] -nuiterations and -norm3diters under FreeSurfer 6.0

2017-08-17 Thread Falk Lüsebrink
Dear Antonio, “-norm3diters“ are the iterations of mri_normalize, whereas “-nuiterations” refers to the number of cycles of mri_nu_correct.mni. I suppose they both work in v6. If not you can simply create a file with expert options. Hope this helps! Best, Falk Von: freesurfer-boun...@nmr.mgh.

Re: [Freesurfer] recon-all with multiple images with different voxel sizes

2017-08-18 Thread Falk Lüsebrink
Dear Gustav, 1. If they have been acquired in the same session with the same protocol, you will increase your SNR by the square root of the number of volumes you use. This can potentially also help in case of minor motions artifacts. However, if your SNR is already high, it's probably be

Re: [Freesurfer] QA tools for FS vs 6.0

2017-08-23 Thread Falk Lüsebrink
Dear Antonietta, I don’t know of any official statement in that regard, however, Yong Li (CC’ed) seems to have updated the QA tools working with FS 6 in April. He may share his code. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auft

Re: [Freesurfer] R: mris_anatomical_stats output

2017-08-30 Thread Falk Lüsebrink
Hi Stefano, never have done this myself, however, have you tried using the -f flag? The helps says this should output the stats to a tablefile. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von std...@virgilio.it Gesendet: Mi

Re: [Freesurfer] How would one run N4 bias corrected T1 and T2 images through FreeSurfer v6.0 REPOST

2018-02-21 Thread Falk Lüsebrink
Hi Eric, I think the easiest way to avoid N3 is to simply add the -nonuintensitycor flag to recon-all and create a symbolic link from nu.mgz to orig.mgz it as otherwise recon-all will end with an error. I'm not sure about the nomenclature of the T2 file, but you should do the same. Best, Falk

Re: [Freesurfer] denoising and recon-all {Disarmed}

2018-10-12 Thread Falk Lüsebrink
External Email - Use Caution Dear Lisa, what you potentially can do is to use the denoised surface (*h.white) as a starting point (instead of *h.orig) in the unfiltered stream. This should remove any bias introduced by the denoising, however, you should gain the advantages of d

Re: [Freesurfer] denoising and recon-all {Disarmed}

2018-10-12 Thread Falk Lüsebrink
I did not find it. Can you attach the link? I would be interested in this information and how to proceed. Thanks in advance, Best, El vie., 12 oct. 2018 a las 13:59, Falk Lüsebrink (mailto:falk.luesebr...@ovgu.de>>) escribió: External Email - Use Caution Dear Lisa, wh

Re: [Freesurfer] autorecon1 with skull stripped image

2018-10-17 Thread Falk Lüsebrink
External Email - Use Caution Dear Rosalia, I’d suggest you run recon-all –autorecon1 with you native data. Then you use mri_mask to mask the T1.mgz with your skull stripped volume to get your desired skull stripping. Name the result brainmask.mgz and continue with recon-all –au

Re: [Freesurfer] Ask for your help about freesurfer submillimeter reconstruction!

2018-10-17 Thread Falk Lüsebrink
External Email - Use Caution Dear Rui, there is no hard limit to resolution. Your data should have a decent quality (no motion artifacts, high SNR, high contrast, isotropic resolution) and the suggestions of the submillimeter reconstruction should give good results. I have run

Re: [Freesurfer] autorecon1 with skull stripped image

2018-10-17 Thread Falk Lüsebrink
, Rosalia El jue., 18 oct. 2018 8:26, Falk Lüsebrink mailto:falk.luesebr...@ovgu.de>> escribió: External Email - Use Caution Dear Rosalia, I’d suggest you run recon-all –autorecon1 with you native data. Then you use mri_mask to mask the T1.mgz with your skull stripped volume to ge

Re: [Freesurfer] Problems to run -autorecon2

2018-10-19 Thread Falk Lüsebrink
External Email - Use Caution Dear Rosalina, you should run recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -autorecon2 and everything will run nicely. You should not include the -i flag again if you want to continue processing your data, as this flag tells FreeSurfer to create

Re: [Freesurfer] Problems to run -autorecon2

2018-10-19 Thread Falk Lüsebrink
Dear Falk, Thank you very much for your email and explanation. It is working now. I wonder how I could set the smoothing for autorecon3 as to run recon -all -all I had the options: -qcache -openmp 8 Kind regards, Rosalia On Fri, Oct 19, 2018 at 2:06 PM Falk Lüsebrink mailto:falk.luesebr

Re: [Freesurfer] Problems to run -autorecon2

2018-10-19 Thread Falk Lüsebrink
’ and I use them in autorecon2 or 3? Best regards, Rosalia On Fri, Oct 19, 2018 at 2:34 PM Falk Lüsebrink mailto:falk.luesebr...@ovgu.de>> wrote: External Email - Use Caution Dear Rosalia, You can specify all flags in every call of recon-all. If this flags does not change any co

[Freesurfer] Voxel size smaller than 1x1x1mm?

2009-03-06 Thread Falk Lüsebrink
Hi Freesurfers, I'm currently doing my bachelors thesis in medical engineering and I'm trying to measure the cortical thickness of scans acquired by a 7T MRT. A colleague of mine has used Freesurfer (v4.0.5) before and mentioned that high resolution scans with a voxel size smaller than 1x1x1mm (

RE: [Freesurfer] Voxel size smaller than 1x1x1mm?

2009-03-11 Thread Falk Lüsebrink
2009 - Does anyone know what to do? Regards, Falk -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, March 06, 2009 1:26 PM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer

Re: RE: [Freesurfer] Voxel size smaller than 1x1x1mm?

2009-03-21 Thread Falk Lüsebrink
cted voxels added... white matter segmentation took 2.4 minutes writing output to wm.seg.mgz... ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 height=320. Regards, Falk Original-Nachricht > Datum: Sat, 21 Mar 2009 10:08:24 +0100 > Von: "Falk Lüs

[Freesurfer] Measuring cortical thickness with high resolution data

2009-03-25 Thread Falk Lüsebrink
Hi Freesurfers, I’m trying to evaluate the usefulness of high resolution scans acquired at 7T with an isometric voxel size of .6mm for the measurement of cortical thickness. The inhomogeneities are taken care of by dividing the scans with another scan of another sequence, so they are not an iss

RE: [Freesurfer] Measuring cortical thickness with high resolution data

2009-04-02 Thread Falk Lüsebrink
tream? Regards, Falk -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: Wednesday, April 01, 2009 7:53 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Measuring cortical thickness with high resolution data Falk, Attached is a mod

RE: [Freesurfer] Measuring cortical thickness with high resolution data

2009-04-06 Thread Falk Lüsebrink
ny flags at all, the error is the same. The unmodified recon-all performs well. Regards, Falk -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Thursday, April 02, 2009 3:28 PM To: Fa

RE: [Freesurfer] Measuring cortical thickness with high resolution data

2009-04-07 Thread Falk Lüsebrink
Hi Doug, Thanks! Now recon-all is processing well. Regards, Falk -Original Message- From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, April 06, 2009 6:25 PM To: Falk Lüsebrink Cc: 'Nick Schmansky'; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer]

RE: [Freesurfer] Measuring cortical thickness with high resolution data

2009-04-08 Thread Falk Lüsebrink
ril 06, 2009 6:25 PM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu; 'Nick Schmansky' Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data Falk, it looks like that file was somehow converted to DOS. try: dos2unix recon-all chmod a+x recon-all then re-

[Freesurfer] aparcstats2table

2009-04-14 Thread Falk Lüsebrink
Hi Freesurfers, I tried using aparcstats2table today and encountered following error message: Trackback (most recent call last): File “usr/share/freesurfer/bin/aparcstats2table”, line 6, in Import fsutils ImportError: No module named fsutils Is anyone able to offer some help?

RE: [Freesurfer] aparcstats2table

2009-04-14 Thread Falk Lüsebrink
Hi Krish, Thanks for your help. Regards, Falk -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Krish Subramaniam Sent: Tuesday, April 14, 2009 5:03 PM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Issues with skull stripping

2009-04-15 Thread Falk Lüsebrink
Hi Freesurfers, I’m currently working on four different subjects and I’m having problems with the skull stripping for three of them. The four subjects I’m trying to process are: 1) 0.6mm iso voxel size, being the same subject as 4) 2) 0.5mm iso voxel size 3) 0.8mm iso voxel

[Freesurfer] Comparison of cortical thickness results

2009-04-27 Thread Falk Lüsebrink
Hi everyone, I’d like to compare the individual cortical thickness results of Freesurfer with the results of another software. The other software measures the cortical thickness for example across the whole left parietal lobe. So I have to get the according value of the whole left parietal lobe

RE: [Freesurfer] Comparison of cortical thickness results

2009-04-28 Thread Falk Lüsebrink
right). then use mris_anatomical_stats to get the stats on this new label. Nick On Mon, 2009-04-27 at 16:31 +0200, Falk Lüsebrink wrote: > Hi everyone, > > > > I’d like to compare the individual cortical thickness results of > Freesurfer with the results of another software.

RE: [Freesurfer] (no subject)

2009-04-29 Thread Falk Lüsebrink
Hi Elina, You could have a look at http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Step-wiseDirectives-1 and http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable to identify the needed time of each process. But I have to mention, that the timeline is not perfectly accurate and can vary

[Freesurfer] Literature values for cortical thickness

2009-05-13 Thread Falk Lüsebrink
Hi everyone, As I don’t do a study in which I compare a group of subjects with some kind of abnormality with a control group I was looking for literature values for cortical thickness. The only paper I found which was written by von Economo et al. in 1925 doing a post-mortem analysis. Are t

RE: [Freesurfer] Literature values for cortical thickness

2009-05-13 Thread Falk Lüsebrink
t: Wednesday, May 13, 2009 2:55 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu; Falk Lüsebrink Subject: Re: [Freesurfer] Literature values for cortical thickness Hi Falk, We do indeed have cortical thickness values for each of the parcellation units for a range of subjects (healthly elderly,

[Freesurfer] Processing high resolution data

2009-05-15 Thread Falk Lüsebrink
Hi FreeSurfers, I’m still trying to process some high resolution data through the freesurfer stream, but it is constantly failing during several different stages. The biggest issue is the skull stripping and I’m still trying to get good results here. Using the –hires switch during –autoreco

RE: [Freesurfer] data conversion

2009-05-15 Thread Falk Lüsebrink
Hi Ali, Try using the –cm switch for mri_convert. This should conform the input not to 1mm iso and 256x256 matrix size, but will conform to the minimum voxel size. The result should be an image having the correct resolution and matrix size. Though you should keep in mind that you will have 320

[Freesurfer] mri_fill

2009-05-18 Thread Falk Lüsebrink
Hi FreeSurfers, At the end of mri_fill I’m told to check the filled volume as the cerebellum may be included. It is and also the brainstem. But actually I don’t know how to fix this. Do I need to include the seed points for cc and pons for better cutting planes? Do I need to manually edit the

RE: [Freesurfer] mri_fill

2009-05-18 Thread Falk Lüsebrink
also tried using seed points, though the cerebellum was never erased. Regards, Falk -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, May 18, 2009 2:07 PM To: Falk Lüsebrink Cc: frees

RE: [Freesurfer] mri_fill

2009-05-19 Thread Falk Lüsebrink
sn't need to be included within FreeSurfer but it would be better if it could handle the .mgz format. Regards, Falk -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Falk Lüsebrink Sent: Monday, May 18, 2009 2:36

RE: [Freesurfer] mri_fill

2009-05-19 Thread Falk Lüsebrink
me voxels, so I think I will stick with it. Thanks in advance, Regards, Falk -Original Message- From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu] Sent: Tuesday, May 19, 2009 5:38 PM To: Nick Schmansky Cc: Falk Lüsebrink Subject: RE: [Freesurfer] mri_fill Falk, I can help you g

[Freesurfer] Guideline to process high resolution data using FreeSurfer and some questions

2009-05-20 Thread Falk Lüsebrink
Hi FreeSurfers, Due to an accident and after several hundreds of hours of work I was finally able to completely (actually not completely, but it seems to work) process high resolution data with an isometric voxel size of 0.6mm without any manual intervention, while using the advantage of all at

[Freesurfer] Troubleshooting

2009-05-28 Thread Falk Lüsebrink
Hello, I’m having trouble to generate a correct aseg.mgz for one volume of mine. The nu_noneck.mgz is also incorrect and therefore I think the -careg stage of autorecon2 might fail. Is there a way to do some kind quality check, like the tal-check during autorecon1, to see whether the talairach.

RE: [Freesurfer] Troubleshooting

2009-05-28 Thread Falk Lüsebrink
Kavec Sent: Thursday, May 28, 2009 1:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting Hi Falk, On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote: > Hello, > > > > I’m having trouble to generate a correct aseg.mgz for one volume of mine. > The nu_

Re: [Freesurfer] Bad aseg

2009-06-29 Thread Falk Lüsebrink
Yes, the skull stripping looks nice. - Original Message - From: "Bruce Fischl" To: "Falk Lüsebrink" Cc: Sent: Monday, June 29, 2009 6:19 PM Subject: Re: [Freesurfer] Bad aseg Did you check the skull stripping? On Jun 29, 2009, at 3:54 AM, F

Re: [Freesurfer] Bad aseg

2009-06-29 Thread Falk Lüsebrink
I could do that, but not before wednesday. - Original Message - From: "Bruce Fischl" To: "Falk Lüsebrink" Cc: Sent: Monday, June 29, 2009 6:53 PM Subject: Re: [Freesurfer] Bad aseg do you want to send us the subject? On Mon, 29 Jun 2009, [UTF-8] Falk Lüsebri

[Freesurfer] Processing data with -noaseg flag

2009-07-30 Thread Falk Lüsebrink
Hi FreeSurfers, As the subcortical segmentation fails fairly often on my high resolution data I want to skip it by using the –noaseg flag, but I’m currently encountering another issue. 1.)During the –fix stage of –autorecon2 I receive following error during mris_euler_numbers (also if I

Re: [Freesurfer] Processing data with -noaseg flag

2009-07-31 Thread Falk Lüsebrink
Behalf Of Bruce Fischl Sent: Thursday, July 30, 2009 2:39 PM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Processing data with -noaseg flag Hi Falk, can you really not afford the 6 minutes or so of scan time to get a good 1mm dataset? We have analyzed a bunch of 7T da

Re: [Freesurfer] mris_fix_topology

2009-08-19 Thread Falk Lüsebrink
20, 2009 12:12 AM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_fix_topology It was not mris_fix_topology that failed but mris_euler_number (but that might have failed because of something in the topology fix). What happens if you: cd /home/falk

Re: [Freesurfer] mris_fix_topology

2009-08-20 Thread Falk Lüsebrink
: Thursday, August 20, 2009 4:44 AM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu; 'Douglas N Greve' Subject: Re: [Freesurfer] mris_fix_topology are you out of disk space? On Thu, 20 Aug 2009, Falk Lüsebrink wrote: > Hi Doug, > > I get the following error: > > rh.orig:

Re: [Freesurfer] mris_fix_topology

2009-08-20 Thread Falk Lüsebrink
uce Fischl Sent: Thursday, August 20, 2009 2:36 PM To: Falk Lüsebrink Cc: freesur...@surfer.nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_fix_topology yes. The only time I've seen this error is when the surface file didn't finish writing. You can load the defects with something l

[Freesurfer] mri_normalize -noconform flag doesn't work in FS 5.0

2010-11-03 Thread Falk Lüsebrink
same. A fix is highly appreciated. Thanks, Falk Lüsebrink ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it

[Freesurfer] -noconform flag of mri_normalize doesn't work

2010-11-09 Thread Falk Lüsebrink
put volume T1.mgz is conformed to 256^3 and therefore to an isotropic resolution of 1mm. This also happens if mri_normalize is used by hand using the -noconform flag. A fix is highly appreciated. Thanks in advance, Falk Lüsebrink ___ Freesurfer mai

Re: [Freesurfer] -noconform flag of mri_normalize doesn't work

2010-11-10 Thread Falk Lüsebrink
ttached is the recon-all.log and the output of mri_info of orig.mgz and nu.mgz. Thanks again, Falk Lüsebrink Original-Nachricht > Datum: Tue, 9 Nov 2010 21:06:49 -0500 (EST) > Von: Bruce Fischl > An: "Falk Lüsebrink" > CC: freesurfer@nmr.mgh.harvar

Re: [Freesurfer] -noconform flag of mri_normalize doesn't work

2010-11-10 Thread Falk Lüsebrink
Hi Bruce, I'm trying to process data with a higher native resolution than 1mm^3 in order to investigate whether a better resolution leads to more accurate results in terms of cortical thickness. Best, Falk Lüsebrink -Original Message- From: freesurfer-boun...@nmr.mgh.harvar