[Freesurfer] R: Re: R: Re: R: R: Re: R: Re: FDR in FS-FAST

yes and this is the error: mri_fdr dyld: Library not loaded: @executable_path/../lib/gcc/lib/libstdc++.6. dylib Referenced from: /Applications/freesurfer/bin/mri_fdr Reason: image not found Trace/BPT trap >Messaggio originale >Da: gr...@nmr.mgh.harvard.edu >Data: 21-dic-2015 20.04

Re: [Freesurfer] Fw: Gray matter intensity

Hi Sabrina you need to tell us what you did the caused the crash. What was the command line? How did you try to load it? cheers Bruce On Mon, 21 Dec 2015, Sabrina Yu wrote: > When I try to load the overlay in freeview, it crashes immediately. Any > thoughts on why this happens? > > Thanks >

[Freesurfer] segmentation fault (core dumped)

Hi Bruce, I have uploaded all the data to the server. The command that I run is 'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'. It would be great if you could keep us updated on how the fixing is going. Thanks!

Re: [Freesurfer] Freesurfer question

Sorry for the delay. Answers below On 12/21/2015 03:58 PM, Woo, Jonghye wrote: > Dear Doug, > > I have following questions: I posted the question but no one answered it. > > 1. What is the best way to convert annotation to the segmentation mask > (volume)? mri_label2vol. Specify the annotation

[Freesurfer] R: Re: R: R: Re: R: Re: FDR in FS-FAST

Thanks but permission denied persist. >Messaggio originale >Da: gr...@nmr.mgh.harvard.edu >Data: 21-dic-2015 17.33 >A: >Ogg: Re: [Freesurfer] R: R: Re: R: Re: FDR in FS-FAST > > >Try this version for mac

Re: [Freesurfer] Fw: Gray matter intensity

no way to help without more info. On 12/21/2015 01:10 PM, Sabrina Yu wrote: > When I try to load the overlay in freeview, it crashes immediately. Any > thoughts on why this happens? > > Thanks > > > From: freesurfer-boun...@nmr.mgh.harvard.edu >

Re: [Freesurfer] Qdec visualization

QDEC cannot but the information may be in the output folder. There should be a file called gammavar.mgh. This will be the standard variance (so take the square root) On 12/21/2015 02:08 PM, John Anderson wrote: > Thanks you very much Doug, > Please one more question. Is there any way in Qdec to

Re: [Freesurfer] FDR in FS-FAST

Not sure. Zeke? On 12/21/2015 02:13 PM, std...@virgilio.it wrote: > yes and this is the error: > mri_fdr > dyld: Library not loaded: @executable_path/../lib/gcc/lib/libstdc++.6. > dylib >Referenced from: /Applications/freesurfer/bin/mri_fdr >Reason: image not found > Trace/BPT trap > > >>

Re: [Freesurfer] Qdec visualization

Hi Doug, Given that the  standard variance can be calculated using the command "mris_calc" and the flag "-sqrt" what is the correct command to do this calculation? I tried:  mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly what I am doing wrong?     Bests, John Sent: 

Re: [Freesurfer] Qdec visualization

why did you not use fscalc, eg, fscalc var.mgh -sqrt -o stderr.mgh On 12/21/2015 03:04 PM, John Anderson wrote: > Thanks Doug, > I used the command "mris_calc gammavar.mgh sqrt" and the output was: > _"Saving result to 'out.mgz' (type = MGH _)" > *Then* I ran the command "mris_calc out.mgz

Re: [Freesurfer] Qdec visualization

Thanks Doug, I used the command "mris_calc gammavar.mgh sqrt" and the output was: "Saving result to 'out.mgz' (type = MGH )" Then I ran  the command "mris_calc out.mgz stats" and the output was :          Size                   [ 163842 ]        Min@(index)        [ 0.00 (161385) ]      

Re: [Freesurfer] Qdec visualization

Thanks you very much Doug, Please one more question. Is there any way in Qdec to get the stamdard error (SE) ?   Bests, John      Sent: Monday, December 21, 2015 at 11:43 AM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec

Re: [Freesurfer] R: Re: R: R: Re: R: Re: FDR in FS-FAST

have you tried changing the permission to be exectuable? chmod a+x mri_fdr On 12/21/2015 02:02 PM, std...@virgilio.it wrote: > Thanks but permission denied persist. > > >> Messaggio originale >> Da: gr...@nmr.mgh.harvard.edu >> Data: 21-dic-2015 17.33 >> A:

Re: [Freesurfer] Qdec visualization

it helps to see the error msg, but my guess is that you need to specify an mgh file, not a txt file. This will give you the voxel-wise stderr, not a standard error for the cluster (which does not make sense) On 12/21/2015 02:38 PM, John Anderson wrote: > Hi Doug, > Given that the standard

Re: [Freesurfer] qdec

Can you run the command below outside of qdec and send us the error it prints to the terminal? asegstats2table --common-segs --meas volume --tablefile /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 100307 101006

Re: [Freesurfer] Help importing files from a previous SPM analysis

you have to do the whole thing On 12/21/2015 06:09 PM, Luis Fernado Silva Castro de Araújo wrote: > Do I have to run recon-all entirely in order to extract volume for a > few Brodmann's areas? Or is there a way of optimizing the process by > striping it of any unneeded calculations? > > It is

Re: [Freesurfer] Error in QDEC -"Generate Stats Data Tables"

can you cut and paste the error into the email rather than sending a jpeg? Your image cut off the most important part On 12/14/2015 09:54 PM, nellie wrote: > > Hi Freesurfer experts, > > When I tried to use *"Generate Stats Data Tables*" in QDEC, some > errors came out. The related screenshot

Re: [Freesurfer] segmentation fault (core dumped)

what server did you upload it to? What is the name of the file? Make sure to include the entire output folder, not just the input files On 12/21/2015 03:33 PM, Fengji Geng wrote: > Hi Bruce, > > I have uploaded all the data to the server. The command that I run is > 'recon-all -all -s $s

Re: [Freesurfer] Help importing files from a previous SPM analysis

Hi Luis sorry, the BA stuff is almost at the very end so you will need to run pretty much everything. We are down to 8 hours or so on modern multi-core CPUs (and even faster than that with 4-8 threads) cheers Bruce On Tue, 22 Dec 2015, Luis Fernado Silva Castro de Araújo wrote: Do I have

Re: [Freesurfer] Help importing files from a previous SPM analysis

Do I have to run recon-all entirely in order to extract volume for a few Brodmann's areas? Or is there a way of optimizing the process by striping it of any unneeded calculations? It is taking 21h to analyze one subject. Best, luis 2015-12-22 9:44 GMT+11:00 Douglas N Greve

Re: [Freesurfer] Help importing files from a previous SPM analysis

Dear Douglas, It's an anatomical analysis. Perhaps I misunderstood the requirement for setting up the directories in the FSFAST for the recon-all command. If that is the case, it is then a matter of converting my img files into mgz and run recon-all on them, am I right? Does the command

Re: [Freesurfer] Help importing files from a previous SPM analysis

If you're doing anatomical analysis, then FSFAST is not needed (nor its directly structure). If you have an input anatomical volume in any format, then just run recon-all -s yoursubjectname -all -i inputfile inputfile can include img but be warned that img does not have information about

Re: [Freesurfer] Fw: Gray matter intensity

Hello, Thank you for the very helpful replies! I have another quick question. Which commands would I use to generate images like the ones in Figure 1 (C) generated in the Salat paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)? Thank you Sabrina

Re: [Freesurfer] Fw: Gray matter intensity

freeview or tksurfer. Load the relevant map as an overlay On 12/21/2015 12:57 PM, Sabrina Yu wrote: > Hello, > > Thank you for the very helpful replies! I have another quick question. Which > commands would I use to generate images like the ones in Figure 1 (C) > generated in the Salat paper

Re: [Freesurfer] Fw: Gray matter intensity

When I try to load the overlay in freeview, it crashes immediately. Any thoughts on why this happens? Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve

[Freesurfer] Qdec

Dear Freesurfer experts, I just started using Freesurfer for performing MRI (T1)- group-based ROI analysis and managed to go through the first recon-all processing stream and making few manual edits. Then I followed first steps of the Qdec -procedure. However, there is a separate section on

Re: [Freesurfer] missing 3volreg.afni

that link works for me. Can you try again? On 12/20/2015 02:17 AM, Thục Trinh wrote: > Hi FS experts, > > I'm working on my fMRI data using FSFAST v.6 tool. But the first step > of Preproc-sess was failed with an error :" *ERROR: cannot find AFNI > command 3dvolreg.afni ". * > I found a thread

Re: [Freesurfer] R: R: Re: R: Re: FDR in FS-FAST

Try this version for mac ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr.osx Use mri_surfcluster (or mri_volcluster) to do the clustering On 12/18/2015 05:11 PM, std...@virgilio.it wrote: > I have run > mri_fdr --help > but I obtained this warning: >

Re: [Freesurfer] Qdec visualization

The correction for multiple comparisons is cluster-based. Each cluster gets a single number. In the display, all the vertices get that same number. On 12/18/2015 03:17 PM, John Anderson wrote: > Hi Freesurfer experts, > I am using Qdec in Freesurfer 5.3 to do some cortical thickness >

Re: [Freesurfer] Z-score from .label

You can use mri_segstats --i z.nii.gz --id 1 --slabel ... On 12/20/2015 08:44 AM, std...@virgilio.it wrote: > Hi list, > > I would like to extract the mean z-score from a roi.label in each > subject after FS-FAST (rs-fMRI seed based). > How can I do? > > Thanks > > > Stefano > > >

Re: [Freesurfer] no aseg.stats after recon-all -all?

here you go. I put rh there too ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lh.DKTatlas40.gcs On 12/18/2015 05:29 PM, Schweren, LJS (med) wrote: > > No, it doesn’t exist (lh nor rh) > > Can I get it somewhere? > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu >

[Freesurfer] Pial Surface, total area?

Hi FS Experts I want to get the total area from pia cortex, in order to normalize the parcellations measure. In lh.aparc.statsfile on there is a line: # Measure Cortex, WhiteSurfArea, White Surface Total Area, ** mm^2 > I've looking for this topic in the lista and I found there is a way to

Re: [Freesurfer] FW: segmentation fault (core dumped)

Hi Fengji hmmm, I don't remember ever seeing a core dump in mri-segstats before. If you upload the entire subject dir (tarred and gzipped) to our ftp site we will fix it. cheers Bruce On Mon, 21 Dec 2015, Fengji Geng wrote: Dear fs experts,  Could anybody help with the error we reported

[Freesurfer] Hippocampal Subfields on 1.5 Tesla - Freesufer v. 6

Hello Freesurfer experts, I am wondering if the new hippocampal subfields (HSF) module that will be included in Freesurfer v. 6 would work with 1.5 Tesla data. Upon reviewing the mail archives, I came across a thread (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35665.html)