[Freesurfer] MNIX/Y/Z coordinates in mri_glmfit-sim .summary file

Hi list, I noticed that, while the wiki refers to Talairach coordinates named TalX/Y/Z (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary), the header in my .summary files reads something like: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWP C

[Freesurfer] Hyppocampal subfields v 6.0 on segmentations with prior versions

Hi List, quick question - can I run the new HyppoSubfields module (v.6.0) on the subject dirs produced by FS 5.3 and/or FS5.1? Or do I need to "re-recon-all" all using FS 6.0 beforehand? Thanks in advance, Nicola ___ Freesurfer mailing list Freesurf

[Freesurfer] Error with mri_glmfit_sim (dev version f)

Hi List, I am getting a couple of strange error when running a 3-group F-test. WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin WARNING: 251446 NaNs found in volume analysis/Ftest/cache.th20.pos.sig.cluster.mgh... And as a result, I consistently get huge clusters: # ClusterNo Max

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

5:38 PM, Douglas N Greve wrote: what is your mri_glmfit-sim command line? On 07/20/2016 05:56 PM, Nicola Toschi wrote: Hi List, I am getting a couple of strange error when running a 3-group F-test. WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin WARNING: 251446 NaNs found in volume

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

: > That is the mri_glmfit command, I need the mri_glmfit-sim. Also, > please do not include variables, just the full command with all > dereferenced args > > On 07/21/2016 03:28 PM, Nicola Toschi wrote: >> Hi, >> >> here it is (I also pasted the mri_glmfit line): >&g

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

opriate since > an F test is unsigned. Also, I would go with a threshold of 2 and not > 1.3. I'm just now finding out that such a low threshold can cause a > lot of false postives on real data. > > > On 07/21/2016 05:32 PM, Nicola Toschi wrote: >> Hi, >> >>

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

Hi Again, (apologies for the many posts): I should add that none of this happens (and everything works fine - no warning and small clusters which look reasonable) if I use version 5.3. Thank you, Nicola On 7/22/2016 2:10 PM, Nicola Toschi wrote: > Hi, > > thanks - I tried using

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

he 2nd. > doug > > On 07/22/2016 08:10 AM, Nicola Toschi wrote: >> Hi, >> >> thanks - I tried using "abs" as well as a higher threshold, however >> the large, whole-brain cluster (as well as the warning messages) >> still remains. >> >>

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

If a dev version, when did you download it? > > On 07/22/2016 12:15 PM, Nicola Toschi wrote: >> Hi Again, >> >> (apologies for the many posts): I should add that none of this >> happens (and everything works fine - no warning and small clusters >> which look reaso

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

a bug. Try this one > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit > btw, you should not be using the dev version of recon-all > > On 07/22/2016 02:01 PM, Nicola Toschi wrote: >> Hi, >> >> it's a dev version downloaded on Jan 17th 2016. &

[Freesurfer] Error with .license after upgrading to 5.2

Hi list, after upgrading to 5.2 (from 5.1), I am consistently getting a license error (see below). The strange thing is that my .license is the same file I was using on 5.1 and worked fine. I have also tried multiple modifications of file permission/owners (its a local install so I can be root

Re: [Freesurfer] Error with .license after upgrading to 5.2

Hi - no luck unfortunately (I had already tried changing permissions) On 03/22/2013 04:09 PM, Varghese Chikku wrote: Hi Nicola, Can you try this command,and echo the license.It may ask for password.I have similar issues with 5.2 and this how i sorted. sudo chmod -R a+rwX /Applicat

Re: [Freesurfer] Error with .license after upgrading to 5.2

Hi, that is exactly what I did (see my first message) - that's why I'm so puzzled! Nicola On 03/22/2013 05:05 PM, Lingqiang Kong wrote: > Just use the license file from your previous version (or you can apply for > a new license for free, but this is redundant). > > cp $OLD_FREESURFER_HOME/.lic

[Freesurfer] License invalid after upgrading OS (opensuse) - still not working

:36 PM, Nicola Toschi wrote: > Hi, > > that is exactly what I did (see my first message) - that's why I'm so > puzzled! > > Nicola > > On 03/22/2013 05:05 PM, Lingqiang Kong wrote: >> Just use the license file from your previous version (or you can apply fo

[Freesurfer] Libray/tool used to read license file - cannot checkout source code

erage/fsaverage.tar.gz Thanks in advance for any pointers. Nicola On 3/26/2013 7:28 PM, Nicola Toschi wrote: > Hi List, > > with reference to my below messages, I have now determined that the > license file is considered invalid by freesurfer executables since i > have upgraded from opensuse 1

Re: [Freesurfer] Libray/tool used to read license file - cannot checkout source code

uple tries) > > -Zeke > > > On 04/02/2013 12:44 PM, Nicola Toschi wrote: >> Hi List, >> >> could anyone point out to me which tool/library is used by freesurfer >> binaries to read the .license file? I am positive my .license file is >> correct (I have us

Re: [Freesurfer] Libray/tool used to read license file - cannot checkout source code

2:08 PM, zkauf...@nmr.mgh.harvard.edu wrote: > Nicola, Akio, and others, > > The issues you experienced with checking out the freesurfer source > code from the CVS repository should be solved. Please let me know if > this is not the case. > > -Zeke > > > > On 04

[Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

Hi Nick, hi List, I have been having the exact same problem (also posted it on this list) with every freesurfer version on Opensuse 12.3, and haven't been able to sort it out. Any luck with it? Any pointers would be highly appreciated. Thanks in advance, Nicola On 5/1/2013 4:42 PM, Nick Jone

Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

is the same one that others have >> seen on Fedora 19 and Ubuntu 13 which is fixed for the upcoming 5.3 >> release. >> >> Nick >> >> >> >> On Tue, 2013-05-07 at 12:15 -0400, Nicola Toschi wrote: >>> Hi Nick, hi List, >>> >>&g

Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

Hi Nick (Schmansky), sorry to jump back in on this thread - I have exactly the same issue (license file not valid) on the same OS (and not on others) with *all* fs commands. I have tried multiple license files from other working installations. Is there anything else i can try? Thanks a lot n

Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

Thanks Nick, well that did change something... here is what i get now with any fs command: /bin/tcsh: /lib64/libfreebl3.so: version `NSSRAWHASH_3.12.3' not found (required by /work2/rootbackup/usr/local/freesurfer/lib/libcrypt.so.1) Should I update/substitute /lib64/libfreebl3.so al well? tha

[Freesurfer] freesurfer@nmr.mgh.harvard.edu

Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (w

[Freesurfer] Downsampling/decimating overlays (not surfaces)

Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (w

[Freesurfer] Downsampling/decimating overlays (not surfaces)

Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (w

Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)

Fischl > wrote: >> Hi Nicola >> >> I think this gets done in the MEG analysis stream, but perhaps Matti >> (ccd) can comment. >> cheers >> BruceOn Thu, 24 Jan 2013, Nicola Toschi wrote: >> >>> Hello list, >>> >>>

Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)

decimated surface, if that's helpful, using > 'mris_curvature_stats' and feeding it the newly downsampled/demicated > surface as input. > > FWIW. > > Best > -=R > > On 1/23/13 18:07 , Nicola Toschi wrote: >> Hello list, >> >> is there a

[Freesurfer] Adding low-res T2 and PD images in the recon-all stream - any advantages?

Hello List, on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually acquire T2 and PD images - however they are at 1x1x5 mm resolution. Would you recommend passing these (T2+PD) to the recon-all stream anyway - would they add value/accuracy to the segmentation/parcellation (or wou

[Freesurfer] Interpretation of pcc.mgh for negative contrasts

External Email - Use Caution Hi List, a dimple question about using partial correlation (pcc.mgh) as effect size measure. I am running multivariate regression and setting positive and negative contrasts one variable at a time, e.g. a design matrix with columns like Intercept

Re: [Freesurfer] Interpretation of pcc.mgh for negative contrasts

(?) gamma.mgh, and negative pcc.mgh withing the same significant cluster? Thanks!!! nicola On 09/13/2018 07:39 PM, Douglas N. Greve wrote: > not sure what your question is. The pcc should have the same sign as the > contrast. > > On 09/13/2018 12:20 PM, Nicola Toschi wrote: >>

[Freesurfer] Workshop on Artificial Intelligence in NMR/MRI and Neuroscience

ducational resource among your local community as well as professional networks. Please, do not hesitate to contact me for more information. Best Regards, Nicola Toschi PS below you can find some social media posts of this annoucement for fast sharing: Twitter: https://secure-web