[Freesurfer] Error using chol

External Email - Use Caution Hi! I am running into an issue with fast_selxavg3b. I am attempting a first level PPI analysis. The command is mkanalysis-sess -fsd bold -native -delay -2/2 -notask -TR 2 -polyfit 6 -analysis [xxx] -funcstem [xxx] -runlistfile mooneyppi.list -nuisreg

[Freesurfer] Cohen's D from selxavg3-sess output

External Email - Use Caution Hi! I would like to compute Cohen's D for individual subjects. I was wondering whether I can use the output from selxavg3-sess for this: ces./rstd Or does this only work with gamma and rstd after mri_glmfit? Thank you, Caspar

Re: [Freesurfer] selxavg3-sess out of memory error

rately. I can't remember whether > it generates a final combined average (been a long time since I used this > option), but run it and see what it does. > > On 6/23/2022 2:00 PM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > Hi! > Any advice on this issu

Re: [Freesurfer] selxavg3-sess out of memory error

ni 2022 um 10:17 Uhr schrieb Caspar M. Schwiedrzik < cschwie...@rockefeller.edu>: > Hi! > I am running large single subject GLMs with selxavg3-sess and I run into a > Matlab "out of memory" error. I was wondering whether you had any advice on > how to get ar

[Freesurfer] selxavg3-sess out of memory error

External Email - Use Caution Hi! I am running large single subject GLMs with selxavg3-sess and I run into a Matlab "out of memory" error. I was wondering whether you had any advice on how to get around that. I have 40-50 runs per subject, and the analyses are whole brain. The GLM

[Freesurfer] PhD student position in the NCC lab at the European Neuroscience Institute Göttingen, Germany

and the names and contact information of two references who are able to comment on your academic background and who agreed to be contacted to Caspar M. Schwiedrzik (cschw...@gwdg.de). The University Medical Center Göttingen is committed to professional equality. We therefore seek to increase the proportion

Re: [Freesurfer] mri_ribbon does not return the ribbon

_ribbon 3 > --label_right_white 41 --label_right_ribbon 42 --save_ribbon yoursubjectname > > > On 5/3/2021 4:31 PM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > Hi! > I am trying to make a ribbon.mgz from a non-human primate surface recon > t

[Freesurfer] mri_ribbon does not return the ribbon

External Email - Use Caution Hi! I am trying to make a ribbon.mgz from a non-human primate surface recon that does not have an aseg. Following this prior discussion: Re: [Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com)

Re: [Freesurfer] cannot find freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3 {Disarmed}

gt; could not find a file. Does that file actually exist? > > On 12/12/2020 3:04 PM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > Hi! > I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am > getting a strange error that I would lo

[Freesurfer] cannot find freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3

External Email - Use Caution Hi! I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am getting a strange error that I would love to get your input on: cannot find freesurfer/average/RB_all_2008-03-26.gca Neither the file nor the path exist. This is the entire

[Freesurfer] unpacksdcmdir in version 7: issues with cfg files

External Email - Use Caution Hi! We are encountering some issues with unpacksdcmdir in version 7.1.1. In particular, it turns out that the handling of cfg files seems to have changed, which makes things somewhat impractical. Old (v5.3) cfg files cannot be used anymore, because

Re: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output {Disarmed}

uple of bits of representation in the conformed ( 1 > byte/voxel) images. Maybe someone else can comment on fixing nu_correct? > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > > *On Behalf Of *Caspar M. > Schwiedrzik > *Sent:* Friday, September 18, 2020 5:04 AM > *

[Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output

External Email - Use Caution Hi! I am having some issue at the interface between mri_nu_correct.mni and mri_normalize, using v5.3. Specifically, the output when applying mri_nu_correct to a T1 is quite dark, with white matter in the range of 15. Contrast is ok. When I apply

Re: [Freesurfer] MEMPRAGE vs. MP2RAGE

> > > > > > Can you elaborate? What are the issues? > > > > Bruce > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> > > *On Behalf Of *Caspar M. Schwiedrzik > > > *Sent:* Mond

[Freesurfer] MEMPRAGE vs. MP2RAGE

External Email - Use Caution Hi! I was wondering whether the issues with surface reconstruction from MP2RAGE data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still persist in more recent releases of Freesurfer, and whether there is information to what extent

[Freesurfer] The European Neuroscience Institute in Göttingen (ENI-G) Germany announces positions for Group Leaders (m/f/d)

External Email - Use Caution The European Neuroscience Institute in Göttingen (ENI-G) Germany announces positions for Group Leaders (m/f/d) - Limitation: fixed-term - Working period: full-time - Tariff: salary according to TV-L - Announcement published on 06.07.2020

[Freesurfer] Scientific Project Coordinator for an open science, large-scale collaboration

External Email - Use Caution Dear all, If you are seeking a challenge, if you are dynamic and enthusiastic about managing a large consortium of scientists, then do not hesitate to apply for the *Scientific Project Coordinator *position in my group at the Max Planck Institute for

Re: [Freesurfer] circular/cyclic color map for polar data in freeview {Disarmed}

External Email - Use Caution Hi! Jumping in on this, since it has come up many times but is without a solution so far: the issue is that the color code is now mapped onto a straight color bar, not a circle. At the same time, it is not documented what color refers to which angle.

Re: [Freesurfer] Notice on freesurfer list archives

External Email - Use Caution Hi! We have a ton of links to the pipermail archives in our wiki. They are all broken now. It seems that the message indices in pipermail do not correspond to those in mail-archive. Is there a way to find the correspondences? Thanks, Caspar Am Do.,

[Freesurfer] Read out N from mri_glmfit outputs?

External Email - Use Caution Hi! Is there a way to read out the N of a fixed effects analysis performed with mri_glmfit? If not, is it safe to assume that it is (number of volumes*number of runs)-excluded time points, summed across subjects? Thanks! Caspar

Re: [Freesurfer] Confidence interval for Cohen's d from gamma/rstd {Disarmed}

d just use the > formula for a gaussian with mean gamma and stddev sqrt(gammavar) > > On 10/5/2019 10:43 AM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > > Hi! > I have an OSGM from a fixed effects group analysis with mri_glmfit. I > would

Re: [Freesurfer] Comparing effects between voxels in a FFX GLM {Disarmed}

10/7/2019 10:32 AM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > Hi Doug, > I would like to test whether an effect that I observed in a given voxel is > larger than in other voxels (this is fMRI data). The additional > complication is that I woul

[Freesurfer] Comparing effects between voxels in a FFX GLM

External Email - Use Caution Hi Doug, I would like to test whether an effect that I observed in a given voxel is larger than in other voxels (this is fMRI data). The additional complication is that I would like to stick as close as possible to the original analysis that yielded

[Freesurfer] Confidence interval for Cohen's d from gamma/rstd

External Email - Use Caution Hi! I have an OSGM from a fixed effects group analysis with mri_glmfit. I would like to calculate the effect size and the 95% confidence intervals. I see from various threads on the mailing list that Cohen's d can easily be obtained from the outputs of

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed} {Disarmed}

External Email - Use Caution following up on this: how do we display complex values from a retinotopy analysis in freeview? thanks! caspar Am Fr., 20. Sept. 2019 um 14:22 Uhr schrieb Caspar M. Schwiedrzik < cschwie...@rockefeller.edu>: > Hi Ruopeng and Doug,

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed} {Disarmed}

iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=NTyTkpnsfZNs76-kCFUYCRUi1-qPnk8BuVBf7GbjOlA=c6QwReyrmeAAZ1CwyRK8EzyjKrOEC31A_WtQLGYuKbs=> > > Best, > Ruopeng > On 9/11/19 9:57 AM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > Hi Doug and Ruopeng, > thanks a lot for

Re: [Freesurfer] timewindow parameter in mkanalysis-sess {Disarmed}

External Email - Use Caution Yes I did. Caspar On Fri, Sep 13, 2019 at 16:19 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Did you put -timewindow before -gammafit ? > > > On 9/12/19 6:08 AM, Caspar M. Schwiedrzik wrote: > > External

Re: [Freesurfer] timewindow parameter in mkanalysis-sess

gt; > On 8/13/19 2:14 PM, Caspar M. Schwiedrzik wrote: > > > > External Email - Use Caution > > > > Hi Doug, > > Thanks for the advice. > > I think the Leite et al. 2002 NeuroImage paper can be interpreted that > > way. See Figure 1 and 2. >

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

quot;Color Wheel" under the > "Color Scale" tab. > > On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote: > > > > External Email - Use Caution > > > > Hi Doug and Roupeng, > > did you already have the chance to look into the question how to > > di

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

External Email - Use Caution Hi Doug and Roupeng, did you already have the chance to look into the question how to display the color wheel with rtview and/or freeview? Thank you! Caspar Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik < csch

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

t; Ruopeng, can freeview display using a color wheel? > > On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > Hi! > I wanted to ask again whether there is a way to display the color wheel in > rtview and/or freeview. We are debugging our

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"

4, 2019 at 14:30 Caspar M. Schwiedrzik < cschwie...@rockefeller.edu> wrote: > Hi! > I am following up on this thread trying to understand how to make the > color wheel visible in rtview, or, if necessary, in freeview. >

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"

External Email - Use Caution Hi! I am following up on this thread trying to understand how to make the color wheel visible in rtview, or, if necessary, in freeview. Thank you! Caspar ___ Freesurfer mailing list

Re: [Freesurfer] mri_surf2surf without sphere.reg {Disarmed}

External Email - Use Caution Thanks Doug, that worked! Caspar Am Di., 3. Sept. 2019 um 17:03 Uhr schrieb Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu>: > Yes, just specify --surfreg white (or some other surface you do have). > > On 9/3/2019 9:51 AM, Caspar

[Freesurfer] mri_surf2surf without sphere.reg

External Email - Use Caution Hi! I am having some issues projecting retinotopic mapping data from a monkey analyzed in surface space onto its surface using rtview. The issue seems to be that the data need to be converted into paint format through mri_surf2surf, and that we do not

[Freesurfer] Two questions about flac_desmat.m for retinotopy analysis in fsfast

External Email - Use Caution Hi Doug, I have two quick questions about the analysis of polar angle maps: 1. Does the analysis take the HRF (lag etc.) into account? 2. Our stimulation starts at 12 for clockwise and counter clockwise. I found this older post

Re: [Freesurfer] timewindow parameter in mkanalysis-sess

. < dgr...@mgh.harvard.edu> wrote: > When you use -gammafit, it automatically sets the time window to 40. If > you really want it at 80, but -timewindow before -gammafit. Do you > really expect the MION hrf to last 80 sec? > > On 8/13/19 11:06 AM, Caspar M. Schwiedrzik wrote: >

[Freesurfer] timewindow parameter in mkanalysis-sess

External Email - Use Caution Hi! I am having difficulties setting the timewindow parameter in mkanalysis-sess in Freesurfer v5.3. I am trying to use 80 (data acquired with MION), but the parameter does not seem to affect analysis.info, where it is always 40. Is it possible to

Re: [Freesurfer] Deconvolution with FSFAST {Disarmed}

TR post onset, etc. > > On 8/9/2019 7:10 AM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > Hi! > I was wondering whether it is possible to do deconvolution of an fMRI time > series with FSFAST? > Specifically, I would like to get a deconvolved sig

[Freesurfer] Deconvolution with FSFAST

External Email - Use Caution Hi! I was wondering whether it is possible to do deconvolution of an fMRI time series with FSFAST? Specifically, I would like to get a deconvolved signal from a region of interest to prepare predictors for a PPI analysis. Additional considerations:

Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

edu>: > Can you send the command line and full terminal output? > > On 5/16/19 5:17 AM, Caspar M. Schwiedrzik wrote: > > > > External Email - Use Caution > > > > Hi! > > We are getting segmentation fault (core dumped) error when trying to > &

[Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6

External Email - Use Caution Hi! We are getting segmentation fault (core dumped) error when trying to run mri_convert on NIFTI files. This is running Freesurfer v5.3 on Centos6, specifically v1.179.2.7 of mri_convert. I suspect that this has to do with libcrypt incompatibilities

Re: [Freesurfer] dimensions swapped with head first-prone acquisition {Disarmed}

> On 5/7/2019 11:27 AM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > > Hi! > I have data acquired on a Siemens scanner with head first-prone. When I > convert the dicom files to MGZ, left and right and superior and inferior, > respectively, ar

[Freesurfer] dimensions swapped with head first-prone acquisition

External Email - Use Caution Hi! I have data acquired on a Siemens scanner with head first-prone. When I convert the dicom files to MGZ, left and right and superior and inferior, respectively, are swapped. The anterior-posterior dimension is ok. I am wondering what the correct way

[Freesurfer] Deadline approaching: Deadline approaching: Neuroscience data analyst (f/m) opening at ENI Göttingen, Germany (new opening)

External Email - Use Caution The European Neuroscience Institute Göttingen (Germany) is seeking a *Neuroscience data analyst (f/m) * initially limited until 31.12.2019 with extension options, full-time | salary according to TV-L The European Neuroscience Institute is looking to

[Freesurfer] Deadline approaching: PhD in visual perceptual learning at the Neural Circuits and Cognition lab @ ENI & German Primate Center Göttingen

External Email - Use Caution The European Neuroscience Institute in Göttingen (ENI-G) Germany, a partnership between the University Medical Center Göttingen and the Max-Planck-Society, is seeking a *Ph.D. student * About us: The Neural Circuits and Cognition lab of Caspar

[Freesurfer] PhD in visual perceptual learning at the Neural Circuits and Cognition lab @ ENI & German Primate Center Göttingen

External Email - Use Caution The European Neuroscience Institute in Göttingen (ENI-G) Germany, a partnership between the University Medical Center Göttingen and the Max-Planck-Society, is seeking a *Ph.D. student * About us: The Neural Circuits and Cognition lab of Caspar

[Freesurfer] memprage processing steps?

External Email - Use Caution Hi! I was wondering whether there is an overview / walkthrough for all the steps involved when working with MEMPRAGE? I am thinking dcmunpack, mri-concat / mri_average, flags for recon-all, mris_make_surfaces, etc. Any pointers would be appreciated.

Re: [Freesurfer] No keyboard input accepted in freeview and tkmedit

nd more than one machine? > > On 06/19/2017 11:59 AM, Caspar M. Schwiedrzik wrote: > > Hi! > > I have a weird issue where tkmedit and freeview both do not accept any > > keyboard input. > > This is Freesurfer v5.3 running on Centos 7, connecting via RDP. > > I saw a cou

[Freesurfer] No keyboard input accepted in freeview and tkmedit

Hi! I have a weird issue where tkmedit and freeview both do not accept any keyboard input. This is Freesurfer v5.3 running on Centos 7, connecting via RDP. I saw a couple of posts by other users having this problem, but I could not find any solutions/replies on the mailing list. Does anyone know

[Freesurfer] separate medial from lateral part in superiorfrontal parcel of Desikan-Killiany atlas

Hi! Is there by any chance a known demarcation line in in the XYZ coordinates of the Desikan-Killiany atlas that could be used to separate the superiorfrontal parcel into a medial and a lateral part? Thanks! Caspar ___ Freesurfer mailing list

Re: [Freesurfer] Freesurfer on Centos 7?

great, thanks! caspar 2016-12-09 16:45 GMT-05:00 : > > To get 5.3 working on machines with perl 5.22 or later I will refer you to > the following thread: > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard. > edu/msg50383.html > > I cant say for sure how

Re: [Freesurfer] Freesurfer on Centos 7?

Thanks for letting me know! What about v5.3? Do I merely need to replace nu_estimate_np_and_em and sharpen_volume, or is there anything else I would need to get it running? Caspar 2016-12-09 16:27 GMT-05:00 : > > The dev version of freesurfer (and the upcoming v6

[Freesurfer] Freesurfer on Centos 7?

Hi! I was wondering whether there is an update from the 2014 thread on Freesurfer's compatibility with Centos 7? The old thread is here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38466.html I have also come across this website mentioning some changes in the installation

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

hared object file: no such file or directory > >> > >> Caspar > >> > >> > >> 2015-11-19 18:49 GMT-05:00 Douglas Greve <gr...@nmr.mgh.harvard.edu > >> <mailto:gr...@nmr.mgh.harvard.edu>>: > >> > >> > >

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

on and > >> let me know if it works? > >> > >> > >> > ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_coreg > >> > >> Thanks, > >> > >> -Zeke > >> > >> > >> &

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

; > >> > > >> > 2015-11-23 14:20 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>: > >> > > >> >> There were some recent changes in the build that eliminated the > >> >> necessity > >> >> for that library. Casper, can you

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

ry mri_coreg instead of fsl? > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg > > > > On 11/19/15 5:25 PM, Caspar M. Schwiedrzik wrote: > > Hi! > I am trying to align a mean EPI volume and a Bruker magnitude map from a > fieldmap measuremen

[Freesurfer] fsl_rigid_register fails with wrong orientation

Hi! I am trying to align a mean EPI volume and a Bruker magnitude map from a fieldmap measurement using tkregister2, fsl_rigid_register and mri_vol2vol. Unfortunately, it seems that somewhere, most likely during fsl_rigid_register, the image orientation get scrambled, and the output has the wrong

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

-03 6:40 GMT-04:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu javascript:; : We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard- i686-stable-pub-v5.1.0 On Thursday, July 30, 2015, Bruce Fischl fis...@nmr.mgh.harvard.edu javascript:; wrote: Hi Caspar

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] Repost: problem with mri_label2label - large amount of holes

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 cschwie...@rockefeller.edu javascript:; : We are using MAC OS 10.9.5 Mavericks

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

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 this and sorry for the delay. The command line we are using is: mri_label2label --srclabel/Volumes/Macintosh_HD/Applications

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

: what is your command line? What do you mean by one anatomy to another? On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote: -- Forwarded message -- From: *Caspar M. Schwiedrzik* cschwie...@rockefeller.edu Date: Thursday, July 16, 2015 Subject: problem with mri_label2label

[Freesurfer] Repost: What algorithm does mri_label2label use?

Hi! We are using mri_label2label to map functionally defined ROIs from one anatomy to another (within subjects), using --regmethod surface. We were wondering which algorithm mri_label2label uses to map the labels? Is it using mri_surf2surf, and if so, which mapmethod is it using? Thanks, Caspar

Re: [Freesurfer] selxavg3-sess CPU limits

the number in newer verisons of matlab, it is either all or one. You can try editing selxavg3-sess to add -singleCompThread to the matlab command line. On 05/28/2015 02:24 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I noticed that selxavg3-sess uses about half of the currently available CPUs

[Freesurfer] ridge regression

Hi! Has anyone tried to use ridge regression on fMRI data (instead of the regular GLM) and would be willing to give some tips? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Whitening in FSFAST

variability and does the whitening in each set of voxels in a bin. doug On 05/12/2015 10:56 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to ask what kind of noise model FSFAST employs for whitening. Is it the one described in Worsley, neuroimage 2002? Is there a place on the wiki

[Freesurfer] Whitening in FSFAST

Hi Doug, I wanted to ask what kind of noise model FSFAST employs for whitening. Is it the one described in Worsley, neuroimage 2002? Is there a place on the wiki or elsewhere where I could find a description? Thanks, Caspar ___ Freesurfer mailing list

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar 2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik cschwie

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

that will work or not. If it runs, you can compare the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works. On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote: Hi Doug, coming back to this once more. I am thinking that I can bypass

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

ok, so the issue is in fast_ldanaflac.m, around line 520: flac.con(nthcon).ContrastMtx_0=[]; that effectively ignores the contrasts that are set up in mystudy. caspar 2014-11-13 17:33 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu : Hi Doug, so I made contrast matrices and stored

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can try in the meantime? Thanks, Caspar 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu : Hi Doug, thanks

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

and the average of the cesvar files, then feed the result into mri_glmfit FFX doug On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: Hi Doug, I wanted to follow up on this. Would you be able to provide a workaround for contrasting multiple taskregs against each other? Is there something I can

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

, Douglas N Greve wrote: It will be the same as the DOF of the individual contrasts (don't sum them). On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar 2014-11-11 12:04 GMT-05:00 Douglas N Greve gr

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

this? Thanks, Caspar 2014-11-11 13:54 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: yes On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu : Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

for an individual, this is problematic but I could probably come up with a work-around. For a group analysis, you can simply compute each taskreg separately, then subtract the two prior to running mri_glmfit. doug On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: Hi! A quick follow-up

[Freesurfer] Running a contrast on multiple taskregs in FSFAST

Hi! I have several external regressors in my analysis that I configure with -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6). I was wondering how to set up mkcontrast-sess to contrast these regerssors given that I do not have a paradigm file for them. Can I just do

[Freesurfer] Quality of surface-based alignment

Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse

Re: [Freesurfer] Quality of surface-based alignment

at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way

Re: [Freesurfer] Quality of surface-based alignment

Nov 2014, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, I should specify that I am working with non-human primate data, so unfortunately, looking at the parcellations would not work. I am aligning individuals to a a custom template that I made. I was wondering whether there is maybe

[Freesurfer] effect size for conjunction analyses?

Hi! I am doing some conjunction analyses (Nichols et al.) on my fMRI data, and I was wondering whether anyone can make a recommendation how to display effect sizes for this kind of analyses? Would you show the effect size estimate corresponding to the p-value that is chosen, an average, or

[Freesurfer] read cluster summary into Matlab?

Hi! I was wondering whether there is code available to quickly read cluster summary files into Matlab? I need access to the cluster-wise p-values. Thank you very much! Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Applications open for the Neurobiology of Cognition GRC/GRS!

(sorry for cross-posting) [image: Gordon Research Conferences] Join us at the 2014 *Gordon Conference* and *Seminar* On *Neurobiology of

Re: [Freesurfer] Anonymizing Siemens DICOM files

From: Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, March 20, 2014 4:29 PM To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Julia Sliwa jsl...@mail.rockefeller.edu Subject: [Freesurfer

[Freesurfer] Anonymizing Siemens DICOM files

Hi Freesurfer Experts, we are looking for a good way to remove subject names and dates of birth from Siemens DICOM headers. Is there something implemented in Freesurfer? Matlab's Image Processing Toolbox has a function to anonymize DICOM files (

[Freesurfer] FSFAST surface-based analysis to w-file

Hi! I need to export results from a surface-based analysis in FSFAST (v5.1) to another program (Caret) that accepts .w files. I was wondering what the recommended way of doing this is. It seems that mri_surf2surf will do the trick? Do I set the source and the target to be the same? Thanks, Caspar

[Freesurfer] Caret F99 to Freesurfer

Hi! This has popped up on the list several times already, but I was wondering whether someone has figured out how to bring the F99 surface atlas from Caret into Freesurfer (not Freesurfer to Caret)? Thanks, Caspar ___ Freesurfer mailing list

[Freesurfer] Problems converting MNC to NII

Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is

Re: [Freesurfer] Problems converting MNC to NII

Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving

Re: [Freesurfer] Problems converting MNC to NII

or so. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote

Re: [Freesurfer] Problems converting MNC to NII

it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange

Re: [Freesurfer] Problems converting MNC to NII

2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values

Re: [Freesurfer] Problems converting MNC to NII

same thing 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3

Re: [Freesurfer] Problems converting MNC to NII

. Schwiedrzik wrote: same thing 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id

Re: [Freesurfer] Problems converting MNC to NII

did not find show up. The data type of the MNC file is unsigned byte; it is read as 32bit integer in Matlab. Caspar 2014/1/22 Douglas N Greve gr...@nmr.mgh.harvard.edu Can you describe the potential problem with mri_binarize more fully? On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote

[Freesurfer] Applying two registration matrices

Hi Freesurfer Experts, I was wondering what the best way to apply two registration matrices to the same data set would be, ideally without re-slicing after the first registration? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] spatialsmooth-sess with option to set mask file name

line when you have one and I'll verify it is the right thing. doug On 01/09/2014 10:21 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I found a way to build it in myself. I am using spatialsmooth-sess from v5.1. I need to smooth some functional data that I have preprocessed through some other

[Freesurfer] spatialsmooth-sess with option to set mask file name

Hi Doug, do you have a version of spatialsmooth-sess with the option to set mask file name? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

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