Re: [Freesurfer] Peak coordinates & Paired t-test with QDEC

Hi Jamie, On 5/24/13 7:18 PM, Jaime Ide wrote: Dear Freesurfer experts: I have two questions: 1) How can I obtain the _peak coordinates_ and _the size_ of the _clusters_ (with uncorrected threshold) visualized in *tksurfer*? (like the tables generated with glmfit-sim) not from tksurfer. You c

[Freesurfer] Peak coordinates & Paired t-test with QDEC

Dear Freesurfer experts: I have two questions: 1) How can I obtain the *peak coordinates* and *the size* of the *clusters*(with uncorrected threshold) visualized in *tksurfer*? (like the tables generated with glmfit-sim) 2) *Is it possible to run paired t-test in QDEC*? I have run Paired Analysi

Re: [Freesurfer] Still confused by group analysis..

On 05/22/2013 01:43 PM, Tudor Popescu wrote: > > > 1) In a design with group and gender as discrete > factors and age > > as a continuous factor, why is it that QDEC only > displays the > > contrast "Does the avg thickness, accounting

Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 34

lications/freesurfer/**fsfast >>>> FSF_OUTPUT_FORMAT nii.gz >>>> SUBJECTS_DIR /Applications/freesurfer/**subjects >>>> MNI_DIR /Applications/freesurfer/mni >>>> FSL_DIR /usr/local/fsl >>>> [dyn1097-8:~] cpellica% mv SetUp

Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 34

still get 'command not >>> found'. >>> What can I try? >>> Thank you, >>> >>> Clelia >>> >>> >>> On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke < >>

Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

Total Gray includes the cerebellar gray doug On 05/24/2013 03:51 PM, Ritobrato Datta wrote: > Hello All, > > Can someone address the following ? I sent this query yesterday but it fell > through the cracks. > > I am using freesurfer 5.1 for my analysis. > > I am interested in calculating the whole

Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf not scaling properly?

Try mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg rawavg.mgz --tval resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6 On 05/24/2013 04:42 PM, Gunter, Geoffrey wrote: > Hello, > > I'm trying to resample Freesurfer output volumes and surfaces back > into their native anatomical spac

Re: [Freesurfer] sig.nii.gz

Hi Dan, it just gets the sign of the contrast it was computed from. You can just take the absolute value. doug On 05/24/2013 03:58 PM, dgw wrote: > Hi, > > I am trying to compare the quality of fMRI data with different > artifact inducing objects in the magnet. I ran expanding and > contracti

Re: [Freesurfer] mri_concat --conjunct

oops, sorry again.It will give the maximum p-value, not the min. This implements Nichols. If you threshold the map at a given level, it will show you what you would have gotten had you applied that threshold to both mapsand then computed an AND. Doing this way means that you can choose your thr

[Freesurfer] resampling surfaces to native space, mri_surf2surf not scaling properly?

Hello, I'm trying to resample Freesurfer output volumes and surfaces back into their native anatomical space using mri_vol2vol and mri_surf2surf. The volumes appear to be resampled correctly, their resolution and orientation match the original images'. However, the resampled surfaces do not ap

Re: [Freesurfer] problem with libreadline.so.5

Not quite... What is the ouput when you type "ls -l libreadline*" in the /lib64 directory? On 05/24/2013 04:23 PM, Erin W. E. Dickie wrote: > Yes I see it in /lib64. So I just need to add /lib64 to the PATH and it > should work? > Thanks, > Erin > > On Fri, May 24, 2013 at 4:18 PM, Z K

Re: [Freesurfer] problem with libreadline.so.5

Hello Erin, libreadline.so is not distributed as part of freesurfer, it should be located somewhere on your system. For example, on CentOS 64bit platforms it can be found in the "/lib64" directory. And on 32bit platforms it can be found in the "/usr/lib" directory. Do you see anything that look

[Freesurfer] sig.nii.gz

Hi, I am trying to compare the quality of fMRI data with different artifact inducing objects in the magnet. I ran expanding and contracting rings and followed the retinotopy fsfast analysis in FreeSurfer 5.1.0. I am trying to compare the data by looking at the sig.nii.gz (which from the website sh

Re: [Freesurfer] tracula mris_resample: Command not found

Stefano, I am able to replicate the issue and I will have to send you a file to fix this. I will send you a fix within the day. -Zeke On 05/23/2013 04:42 PM, std...@virgilio.it wrote: > Hi Anastasia, > > I'm re-running tracula by using new version 5.3. > > In the step 3 (trac-all -inter -c $FRE

[Freesurfer] Repost: question abt supratentorial vol and total brain vol.

Hello All, Can someone address the following ? I sent this query yesterday but it fell through the cracks. I am using freesurfer 5.1 for my analysis. I am interested in calculating the whole brain vol (total Gray vol + total WM vol) excluding the CSF volume and cerebellum. Total Brain Vol

Re: [Freesurfer] tkmedit BUS error

Hi Amber, See the following wikipage which I created to troubleshoot various GUI issues. Specifically the second issue down which addresses the "Bus Error". https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting -Zeke On 05/24/2013 03:26 PM, Amber M Gregory wrote: > I am ha

[Freesurfer] tkmedit BUS error

I am having a problem using tkmedit and tksurfer with Freesurfer. Freeview is working. Below is the tkmedit error and relevant specs. Any suggestions are welcome. General Specs Apple OS 10.6.8 Processor: 2x 2.26 Ghz Quad-core Intel Xeon 16 GB DDR3 Freesurfer Ver 5.3.0 Chipset Model:NVIDIA Ge

Re: [Freesurfer] mri_concat --conjunct

Hi Doug, I also have a tendency towards correcting the conjunction map. Regarding mri_concat: If I understand the results correctly, it does not exactly implement Nichols. It seems to give voxels even if they are only significant in one contrast, which is exactly what Nichols et al argued against.

Re: [Freesurfer] 'Bus error' when running commands from the "Testing your FreeSurfer Installation" wiki page

Hi Max, See the following wikipage which I created to troubleshoot various GUI issues. https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting -Zeke On 05/24/2013 02:56 PM, Swartz, Max wrote: > Happy Friday! > > I was able to install FreeSurfer v5.3.0 on my personal Macbook (

Re: [Freesurfer] mri_concat --conjunct

oops, sorry, mri_concat takes the smallest p-value (and so implements Nichols). I think I'd to the multiple comparisons correction after conjunction (but I'd like to hear opinions). Not sure about the FWHM, probably take the max of the contrasts that go into it. doug On 05/24/2013 03:02 PM,

Re: [Freesurfer] mri_concat --conjunct

Hi Doug, just to make sure I understand you right: No matter whether I want to test a conjunction a la Friston (any voxel significant, this is what mri_concat gives) or a la Nichols (both voxels significant), I would take the maximum p-value, correct? What about multiple comparisons? Would you thre

[Freesurfer] 'Bus error' when running commands from the "Testing your FreeSurfer Installation" wiki page

Happy Friday! I was able to install FreeSurfer v5.3.0 on my personal Macbook (2.4 GHz Intel Core i5 processor, 4 GB 1067 MHz DDR3, Mac OS X 10.6.8). Unfortunately, I'm still getting some error messages as I run through the commands on the "Testing your FreeSurfer Installation" page in the manual.

Re: [Freesurfer] FreeSurfer v 5.3.0 compatibility with Mac OS X 10.4.11

Thanks! On Fri, May 24, 2013 at 12:37 PM, Z K wrote: > Max, > > All of Sebastian's answers below are accurate. Unfortunately their are no > no immediate plans to build a PowerPC compatible version of freesurfer. You > choice is to either use a different Mac with an intel chip or download > free

Re: [Freesurfer] Bug report: QDEC

Yes, I am sure. For instance, with FDR at 0.95, I see the following in the terminal: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.95, vwth=1.63965 Found 3954 of 163842 vertices above FDR threshold (of 1.63965) I then change FDR to 0.05, and the terminal brings out two more lines which are i

Re: [Freesurfer] command not found

Clelia, Please type the following commands in the terminal window and provide us any error message you may receive. >> setenv FREESURFER_HOME /Applications/freesurfer >> source $FREESURFER_HOME/SetUpFreesurfer.csh >> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz If a window with an ima

Re: [Freesurfer] mri_concat --conjunct

The way to do it is to take the maximum p-value at each voxel (this is what mri_concat does). doug On 05/24/2013 02:10 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > I am trying to implement something like the MS/CN conjunction > suggested by Nichols. > For that, I am finding the voxels that sho

Re: [Freesurfer] p-value visualization

Here is an example regionaldata file. (File with script and dependency is being held for moderator approval) Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research

Re: [Freesurfer] mri_concat --conjunct

Hi Doug, I am trying to implement something like the MS/CN conjunction suggested by Nichols. For that, I am finding the voxels that show a significant effect at a given threshold in both contrast maps. I have one question about the resulting p-value. In principle, I would tend to think that the con

Re: [Freesurfer] FreeSurfer v 5.3.0 compatibility with Mac OS X 10.4.11

Max, All of Sebastian's answers below are accurate. Unfortunately their are no no immediate plans to build a PowerPC compatible version of freesurfer. You choice is to either use a different Mac with an intel chip or download freesurfer v5.1 which is PowerPC compatible from this link: ftp://su

Re: [Freesurfer] problem with alignment of labeling files generated from the rh.area file

Hi Tina, I don't really understand what you mean by offset. Do you mean when you visualize on the surface? The placement is completely dictated by the index you assign in that case. If you are doing this in matlab, make sure you account for the fact that the vertex numbers are 0 based not 1-ba

Re: [Freesurfer] command not found

Hi Louise, yes, teh FreeSurfer related commands are still not found. The other thing is that I had problem with license file. I have created a file in Applications/Freesurfer named .license and tried to copy inside le license key but I'm not sure that it worked beacuse if I write cd .license I get

Re: [Freesurfer] p-value visualization

We don't have a binary that does it. You can do it in matlab, but it will take a bit of programming. doug On 05/24/2013 10:54 AM, Ludovici, Katharine (NIH/NIMH) [F] wrote: > Hello, > > We are attempting to compare surface area for 46 regions of interest in > subjects versus controls. We've cre

Re: [Freesurfer] A question of running fsfast in mac

Hi Sharon, you have to specify an analysis (as created by mkanalysis-sess) as the argument to -analysis doug On 05/24/2013 10:35 AM, Yongxia Zhou wrote: > Dear Freesurfer experts: > hi, I'm one of the attendees of the multi-modality training program. I > had tried running fsfast in the mac

Re: [Freesurfer] command not found

Hi Clelia, That mv command is failing presumably because SetUpFreeSurfer.txt does not exist in that directory. What are you trying to do with the mv command? It does look like freesurfer was sourced successfully. Are the FreeSurfer related commands still not found? Don't forget to cc the f

Re: [Freesurfer] problem with alignment of labeling files generated from the rh.area file

Doug can you answer this? The vertex indices can be fixed with matlab but more importantly I need to know why there is a slight offset in vertex coordinates. Thank you! Tina Jeon -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 23, 2013 10

[Freesurfer] p-value visualization

Hello, We are attempting to compare surface area for 46 regions of interest in subjects versus controls. We've created a list of p-values for each ROI using R Studio to compare the two groups. Is there any way to visualize these p-values mapped on to the ROI's? Thanks very much, Katie Ludovic

[Freesurfer] A question of running fsfast in mac

Dear Freesurfer experts: hi, I'm one of the attendees of the multi-modality training program. I had tried running fsfast in the mac and got an error message. Below is the detail information. Any of your suggestions is highly appreciated and thank you very much. -Sharon OS: Mac OS X 10.5.6 [Yongxi

Re: [Freesurfer] command not found

Hi Clelia, What do you run to source FS and do you get any output in your terminal after doing so? What operating system are you running? You might try using c-shell instead of bash. -Louis On Fri, 24 May 2013, clelia pellicano wrote: Hi Louis, thank you for your answer.  I sourced freesur

Re: [Freesurfer] FreeSurfer v 5.3.0 compatibility with Mac OS X 10.4.11

Hi Max, not speaking for the fressurfer developers, just as a user like yourself... On May 24, 2013, at 00:58 , Swartz, Max wrote: > Hello, > > I am working as a research assistant for the summer with the University of > Cincinnati's Psychiatry department in the Division of Bipolar Disorders

Re: [Freesurfer] recon-all with FLAIR error no FSL installed

Hi Veronica BBR can use FSL or SPM to initialize, although we'll probably add an option in the future to use some things that Martin Reuter and Christian Wachinger are working on. How did the refinement work? We've only run it on a handful of cases, so it's pretty bleeding edge and I'm interes

[Freesurfer] Rejoindre mon réseau sur LinkedIn

LinkedIn Melina Papalampropoulou-Tsiridou souhaite se connecter à vous sur LinkedIn : -- Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Melina Papalampropoulou-Tsir