[Freesurfer] Freesurfer version after 5.3.0 from May 2013?

Hi all, I am a little confused about what the latest Freesurfer version is. I thought that v5.3.0 from May 15, 2013 would be the latest, but today I saw in the Tracula update list that there is apparently a version from December 9, 2013. Could you please clear that up for me? Thanks, Janosch

[Freesurfer] missing Freesurfer wiki pages

Dear all, Most of the links on https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction page do not work. If I clik for example on FsTutorial/SkullStripFix the following message will popup: "This page does not exist yet. You can create a new empty page, or use one of the page templates.

[Freesurfer] mris_make_face_parcellation

Hi Freesurfer experts, I first parcellated the ?h.aparc.annot using the mris_divide_parcellation and at first glance it seems fine. However, I experienced that the size of the regions varies a lot. I then found the mris_make_face_parcellation, that parcellate the surface in regions of more equ

[Freesurfer] preprocessing question

Dear freesurfers, I have installed freesurfer and fsl on my Mac: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_F

Re: [Freesurfer] FWHM in mri_glmfit-sim

Hi Doug, Thank you for your advice. Would you also have any advice on what would be the correct process to follow if volume based smoothing at subject level(4mm) and surface based smoothing at group level(4mm) are applied? Many thanks, Mariam. On 31 Mar 2014, at 16:36, Douglas N Greve wrote:

Re: [Freesurfer] preprocessing question

Hi! Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) What happens if you type in your terminal fslmaths ? Best, Markus 2014-04-01 9:59 GMT+02:00 Eiran Harel : >Dear freesurfers, > I have installed freesurfer and fsl on my Mac: > > * freesurfer-Darwin-snowleopard-i686

Re: [Freesurfer] preprocessing question

Hi Markus, Thanks, i did install fsl and when i type fslmaths it gives me the help for that command. Any other suggestions? Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gsch

Re: [Freesurfer] preprocessing question

Hi, what does it say when you type which fsl which fslmath ? It mud be the same thing as FSL_DIR /usr/local/fsl It is possible that the FSL_DIR specified in the freesurfersetup is not the good one... Best, Markus 2014-04-01 10:25 GMT+02:00 Eiran Harel : > Hi Markus, > Thanks, i

Re: [Freesurfer] preprocessing question

Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? EIran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 12:55 PM To: Fre

[Freesurfer] Fwd: Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table

- Mensagem encaminhada de _andre...@sapo.pt - Data: Mon, 31 Mar 2014 14:45:00 +0100 Hello! I'm reposting my email without attachments this time since it is not getting to the list if I have attachments. Could you advice please? Thank, Andreia - Mensagem encaminhada de _an

Re: [Freesurfer] preprocessing question

Hi, Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that can be used in FSL, I think it is not necessary to have matlab working for FSL to work. There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab). The error message tells you that freesurfer doesn't fin

Re: [Freesurfer] mris_make_face_parcellation

Hi Karen sorry, I don't think so. You could certainly discard parcels that have a substantial non-cortical component to them, but parcellating the remainder of the surface uniformly isn't trivial. cheers Bruce On Tue, 1 Apr 2014, Karen Marie Sandø Ambrosen wrote: Hi Freesurfer experts, I

Re: [Freesurfer] Fwd: Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table

Hi Andreia the thing to look for is if the pial surface is missing a fold that the white matter surface captures. Or maybe the white matter surface really is less smooth than the pial one, which would lead to a larger surface area. cheers Bruce On Tue, 1 Apr 2014, _andre...@sapo.pt wrote: >

Re: [Freesurfer] quality T1 scans for new study

Hi Jelmer if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc). We also have recommended morphometry sequences on our website. 10 min is a pretty long structural scan for a modern MRI sc

[Freesurfer] Apply talairach.xfm to orig.mgz

Hi everybody, I'm in the process of studying all the Recon-all steps to find the step that is giving me problems in my study. Now I've just run the -talairach input and I would like to see if the talairach.xfm came out correctly by applying it to my ORIG.mgz, how can it do it? Which command do I h

Re: [Freesurfer] Apply talairach.xfm to orig.mgz

Hi Francesco look at mri_vol2vol -help and search for talairach. It has an explicit option for this (--tal). Or you can do it directly in tkregister2 if all you want to do is visualize the results of applying the transform (this is also in the mri_vol2vol help) cheers Bruce On Tue, 1 Apr 201

Re: [Freesurfer] quality T1 scans for new study

Hi Bruce, Thanks for your fast reply. Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient). Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocol

[Freesurfer] Invalid license when run recon-all

Dear FS experts,I want to report an error:I have installed FreeSurfer in my another computer using my license file which works in my old computer. But when I run “recon-all” its shown --ERROR: Invalid FreeSurfer license key fou

Re: [Freesurfer] quality T1 scans for new study

looks pretty reasonable. Andre: any comments/suggestions? On Tue, 1 Apr 2014, Kok, JG (neuro) wrote: Hi Bruce, Thanks for your fast reply. Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient). Checking it with the inf

Re: [Freesurfer] preprocessing question

Hi Markus, [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% more $FSL_DIR/etc/fslversion 5.0.6 [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% echo $FSLDIR /usr/local/fsl Thanks! Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-b

Re: [Freesurfer] quality T1 scans for new study

No, I think that's a reasonable protocol to use and good to use SENSE to speed it up. Original message From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study l

Re: [Freesurfer] preprocessing question

Well, Eiran, That seems all fine. Maybe Bruce or Doug can jump in and help? Sorry! Markus 2014-04-01 15:25 GMT+02:00 Eiran Harel : >Hi Markus, > > [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% > more $FSL_DIR/etc/fslversion > 5.0.6 > [Eran-Harels-MacBook-Pro:/Ap

Re: [Freesurfer] Invalid license when run recon-all

Can you please send me the license file that you are trying to use (as an attachment) directly to my email address, and not to the freesurfer list. Then I can give it a try. Thanks. -Zeke On 04/01/2014 08:20 AM, gong jinnan wrote: > Dear FS experts, > I want to report an error: > I have install

Re: [Freesurfer] preprocessing question

I'll defer to Doug/Zeke/Nick on this one Bruce On Tue, 1 Apr 2014, Eiran Harel wrote: Thanks Markus. Doug, Bruce, any suggestions? Eiran   From: freesurfer-boun

Re: [Freesurfer] preprocessing question

Thanks Markus. Doug, Bruce, any suggestions? Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.com] Sent: Tuesday, April 01, 2014 4:40 PM To: Freesurfer support lis

Re: [Freesurfer] Apply talairach.xfm to orig.mgz

Thanks, I'll try with tkregister2 as I want to just check talairach and not use it elsewhere. Still thanks for the help and quickness, Francesco Baldacchini 2014-04-01 14:18 GMT+02:00 Bruce Fischl : > Hi Francesco > > look at mri_vol2vol -help and search for talairach. It has an explicit > opti

Re: [Freesurfer] ROI analyses

Hi Doug, I am able to run mri_segstats with slabel below, but it is finding two segmentations in my label and producing a column for each. one is associated with an ID of 0 and one is associated with an ID of 1. I assume that I want the 2nd column (the ID of 1). What is the command doing? Is it

Re: [Freesurfer] quality T1 scans for new study

Hi Bruce and Andre, Many thanks for your comments! Cheers, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Andre van der Kouwe [an...@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl

[Freesurfer] native or fsaverage spherical space for distance measures?

Dear Freesurfers, according to my research and 'playing-around' with Freesurfer tools on measuring distances between vertices or peak voxels, I'm still unsure about the most adequate way of comparing distances between peak voxels corrected for folding patterns. To my current knowledge, I figur

Re: [Freesurfer] Longitudinal Analysis Questions

Hi Panos, 1. you need to edit the base. That is actually more important than editing the individual (cross) time points from the first stage, especially when the edits are supposed to improve the surface. The reason is that the surface is taken from the base to initialize all time points in th

Re: [Freesurfer] Freesurfer version after 5.3.0 from May 2013?

Hi Janosch - The December 9th tracula update is just that, an update to the tracula code without any changes to the rest of freesurfer. a.y On Tue, 1 Apr 2014, Janosch Linkersdörfer wrote: Hi all, I am a little confused about what the latest Freesurfer version is. I thought that v5.3.0 fr

Re: [Freesurfer] SEEDING in Tracula

Hi Emily - I don't remember off the top of my head where this is mentioned, but it probably refers to the FA, MD, etc maps. An ROI-based analysis would be one where you average the FA in an ROI, so it doesn't refer to tractography. Hope this helps, a.y On Mon, 31 Mar 2014, ebell...@uwm.edu

Re: [Freesurfer] quality T1 scans for new study

Dear Bruce and Andre, PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine... Thanks, Je

Re: [Freesurfer] quality T1 scans for new study

no, I just looked at the ones in the body of your email On Tue, 1 Apr 2014, Kok, JG (neuro) wrote: Dear Bruce and Andre, PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would

Re: [Freesurfer] ROI analyses

Use --id 1 or --excludeid 0 with mri_segstats. 3rd question answered below. On 04/01/2014 10:42 AM, Emily Boeke wrote: > Hi Doug, > > I am able to run mri_segstats with slabel below, but it is finding two > segmentations in my label and producing a column for each. one is associated > with an I

Re: [Freesurfer] FWHM in mri_glmfit-sim

If I could not reanalyze the data, I would just follow the standard process. doug On 04/01/2014 04:12 AM, Mariam Sood wrote: > Hi Doug, > Thank you for your advice. Would you also have any advice on what would be > the correct process to follow if volume based smoothing at subject level(4mm) >

Re: [Freesurfer] quality T1 scans for new study

Hi Andre, I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is referring to were the suggested parameters in "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recomm

Re: [Freesurfer] preprocessing question

does $FREESURFER_HOME/bin/fslmaths.fsl exist? On 04/01/2014 03:59 AM, Eiran Harel wrote: > > Dear freesurfers, > I have installed freesurfer and fsl on my Mac: > * > * > * freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 * > *Setting up environment for FreeSurfer/FS-FAST (and

Re: [Freesurfer] preprocessing question

Hi Doug, No, it does not exist. What should i do? Thanks, Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: freesur

[Freesurfer] Gray to White Matter Intensity Ratio

Dear FreeSurfers, The pctsurfcon calculates the contrast between the white and gray matter using the formula below and saves the output in the ?h.w-g.pct.mgh file, which can be used for analysis. 100*(W-G) pct = - 0.5*(W+G) However, I would like to get separate

Re: [Freesurfer] Freesurfer version after 5.3.0 from May 2013?

Thanks, Anastasia! Am 01.04.2014 um 17:36 schrieb Anastasia Yendiki : > > Hi Janosch - The December 9th tracula update is just that, an update to the > tracula code without any changes to the rest of freesurfer. > > a.y > > On Tue, 1 Apr 2014, Janosch Linkersdörfer wrote: > >> Hi all, >> >>

Re: [Freesurfer] Gray to White Matter Intensity Ratio

The easiest way would be to edit pctsurfcon in the following way Change set wm = $tmpdir/$hemi.wm.$ext To set wm = $outdir/$hemi.wm.$ext and set gm = $tmpdir/$hemi.gm.$ext To set gm = $outdir/$hemi.gm.$ext This will create ?h.wm.mgh and ?h.gm.mgh in subject/surf doug On 04/01/201

Re: [Freesurfer] preprocessing question

That is weird. You can get a copy from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac copy it to $FREESURFER_HOME/bin/fslmaths.fsl On 04/01/2014 12:25 PM, Eiran Harel wrote: > Hi Doug, > No, it does not exist. > What should i do? > Thanks, > Eiran > ___

Re: [Freesurfer] Gray to White Matter Intensity Ratio

Thank you And how could I get the ratio of gm/wm at each vertex, rather than the pct? Nenad On 2014-04-01 17:32, Douglas N Greve wrote: > The easiest way would be to edit pctsurfcon in the following way > > Change >set wm = $tmpdir/$hemi.wm.$ext > To >set wm = $outdir/$hemi.wm.$ext >

[Freesurfer] displaying annotations on inflated brain in freeview

Hi, I'm having trouble displaying annotations on inflated brains in freeview. I have loaded and selected the inflated surface and annotation for that subject, but nothing shows up on the brain. I have had no trouble displaying annotations on the pial surface of the brain. Thank you for your time

Re: [Freesurfer] FWHM in mri_glmfit-sim

Thanks very much Doug. Mariam. On 1 Apr 2014, at 17:17, Douglas N Greve wrote: > > If I could not reanalyze the data, I would just follow the standard process. > doug > > On 04/01/2014 04:12 AM, Mariam Sood wrote: >> Hi Doug, >> Thank you for your advice. Would you also have any advice on wha

Re: [Freesurfer] preprocessing question

Thanks, i can't open the page: Safari can’t open the page “ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac” because Safari can’t load any data from this location. What is the problem? Eiran From: freesurfer-boun...@nmr.mgh.ha

Re: [Freesurfer] Gray to White Matter Intensity Ratio

try fscalc lh.gm.mgh div lh.wm.mgh -o lh.ratio.mgh doug On 04/01/2014 12:42 PM, N. Medic wrote: > Thank you > > And how could I get the ratio of gm/wm at each vertex, rather than the > pct? > > Nenad > > > On 2014-04-01 17:32, Douglas N Greve wrote: >> The easiest way would be to edit pctsurfcon

Re: [Freesurfer] Gray to White Matter Intensity Ratio

Thanks again, it worked Nenad On 2014-04-01 17:58, Douglas N Greve wrote: > try > fscalc lh.gm.mgh div lh.wm.mgh -o lh.ratio.mgh > > doug > > On 04/01/2014 12:42 PM, N. Medic wrote: >> Thank you >> >> And how could I get the ratio of gm/wm at each vertex, rather than the >> pct? >> >> Nenad >

Re: [Freesurfer] preprocessing question

try now On 04/01/2014 12:53 PM, Eiran Harel wrote: > Thanks, i can't open the page: > Safari can’t open the page > “ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac” > because Safari can’t load any data from this location. > What is the problem? > Eiran > ___

Re: [Freesurfer] Longitudinal Analysis Questions

Hi Martin, Thanks for your reply! Yes, that definitely makes sense. I had an additional probably elementary question: I tried to reconstruct the base after I added some control points to it, using the command recon-all -autorecon2-cp -autorecon3 -subjid but the following error pops up: ERROR: I

[Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

Hello, I have run mri_annotation2label and then selected the labels corresponding to my ROI, creating a new annotation file using mris_label2annot. When I load my new annotation file in freeview, the ROI's are displayed nicely in different colors. However the remainder of the brain is dark black

Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

What was your mris_label2annot command line? What was the terminal output? Can you send the colortable file you passed with --ctab? doug On 04/01/2014 02:25 PM, Laura Taylor wrote: > Hello, > > I have run mri_annotation2label and then selected the labels > corresponding to my ROI, creating a

Re: [Freesurfer] Pial surface error

Hi Eleanor what version are you running? Do you see that in tkmedit? I kind of remember a strange display bug that was in freeview that caused this type of thing. Can you download a new version and see if it is any better? Or see if it goes away in tkmedit thanks Bruce On Tue, 1 Apr 2014, Ele

[Freesurfer] question about running a post-hoc group analysis

Hello, I'm working with a data set which has been analyzed entirely in the subjects' native spaces in Freesurfer, but now I would like to run a group analysis on the data. Is it necessary to re-run the preprocessing and contrasts in normalized space, or is there a small set of files that are looke

[Freesurfer] mri_glmfit question

Dear all, I am trying to run a group analysis between 2 groups of subjects. I did the mris_preproc and mri_surf2surf steps. When I set up my mri_glmfit, the end of the output is: Reshaping mriglm->mask... search space = 74485.691578 DOF = 1344 Starting fit and test Fit completed in 0

Re: [Freesurfer] preprocessing question

Thanks Doug, I notice that on my Mac build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 ...I don't have fslmaths.fsl neither. There are only $ which $FREESURFER_HOME/bin/fsl* > /Applications/freesurfer/bin/fsl_label2voxel > /Applications/freesurfer/bin/fsl_rigid_register > /Applications/

Re: [Freesurfer] question about running a post-hoc group analysis

isxconcat-sess should take data in the native space doug On 04/01/2014 04:32 PM, Terri Scott wrote: > Hello, > > I'm working with a data set which has been analyzed entirely in the > subjects' native spaces in Freesurfer, but now I would like to run a > group analysis on the data. Is it necessary

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

Did you look at the mri_glmfit-sim --help yet? On 04/01/2014 04:42 PM, Tudor Popescu wrote: > Sorry I know that our questions often have an answer in the > documentation, but this case does not seem straightforward. I ran the > following command > mri_glmfit-sim --glmdir > /media/math/all

Re: [Freesurfer] mri_glmfit question

what does the max vox have to do with the search space? I'm not sure what the problem is here. dough On 04/01/2014 05:05 PM, Govindarajan, Koushik Athreya wrote: > > Dear all, > > I am trying to run a group analysis between 2 groups of subjects. I > did the mris_preproc and mri_surf2surf steps.

Re: [Freesurfer] preprocessing question

thanks, it must be something in our distribution script affecting mac On 04/01/2014 05:13 PM, Markus Gschwind wrote: > Thanks Doug, > > I notice that on my Mac > build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 > > ...I don't have fslmaths.fsl neither. There are only > > $ which $FR

Re: [Freesurfer] mri_glmfit question

I proceeded to do a Monte Carlo simulation with this glm and pretty much the entire brain lit up. That is why I was wondering if the max vox being so large or the search space has anything to do with it. I used a vertex-wise p-value of 0.001 and a cluster-wise p-value of 0.05. Thanks Koushik

Re: [Freesurfer] Fwd: Questions aobut using monte carlo sim in Qdec

On 04/01/2014 05:40 PM, Ashley Shurick wrote: > Hi all, > > What is the default cluster-wise threshold in qdec for monte carlo > simulations? My output says the area threshold is 0mm^2, which doesn't > make sense (see attachment). the threshold is .05. The minimum area threshold is ignored in fa

Re: [Freesurfer] mri_glmfit question

No it should not. You should check your data and design to make sure that it makes sense doug On 04/01/2014 05:46 PM, Govindarajan, Koushik Athreya wrote: > I proceeded to do a Monte Carlo simulation with this glm and pretty much the > entire brain lit up. That is why I was wondering if the max

Re: [Freesurfer] recon all with 7T data

hi Xiaomin, 7T data can sometimes cause Talairach failures with the standard registration tools due to the strong bias fields. the Talairach transformation is used for identifying seed points, and the -use-mritotal flag just specifies that the MINC software will be used for the Talairach'ing. se

[Freesurfer] Cortical thickness measurement using Freesurfer v 5.3

Hello Freesurfer Expert, I am trying for measurement of cortical thickness using Freesurfer v5.3. I have getting values for cortical thickness, surface area and gray matter volume using stats/rh.aparc.a2009.stats file. But i am looking for general value for entire Frontal,Temporal, parietal and oc