[Freesurfer] Longitudinal analysis with QDEC

[Wrobel, Pawel]

Hello Dear FreeSurfer Developers,

Thank You once again for helping me a couple of months ago. Today I came across 
a new obstacle, as I have been trying to analyse longitudinal material.
I have performed all preparation steps and I started performing statistical 
analysis in Qdec when receiving following message:

Error in Analyze: Couldn't open 
.../FreeSurfer_output/subjects/CT_10/BLD013_/surf/lh.thickness.fwhm15.fsaverage.mgz
 or .mgh file.

I have checked in the surface directory and I could not find this file. There 
were several variations of it, but not a file with this particular name.

I have been working with Freesurfer5.3.

Thank You for Your help!
Pawel

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Re: [Freesurfer] Issue opening .dmg file for installing freesurfer patch/code addition for brainstem. Error is "image not recognized"

[zkaufman]

My guess is that you are using Safari on a Mac OSX Machine? If so, I have
observed that Safari  has strange behavior with ftp links. Can you try
using another browser like Firefox or Chrome? Or, you can download by
typing the following command in a terminal window:

  $> curl -O
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-OSX-dev.dmg

Hope this helps.

-Zeke


> Hello,
>
> I'm trying to segment the brainstem into subparts. I found online for
> freesurfer 5.3 you can use the following link to install the need codes:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
>
>
> which was from the following freesurfer question/solution:
>
>
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42064.html
>
> However, when I open the ftp as a guest and try to open the .dmg file I
> get
> the error "image not recognized". Looking into why this happens it sounds
> like the download went bad. I've tried re-downloading the file a few times
> and am now wondering if the uploaded file was bad? Is there another
> solution so I can segment the brainstem?
>
> Thank you for your help,
>
> Jon
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Re: [Freesurfer] Longitudinal analysis with QDEC

[Martin Reuter]

Hi Pawel,

your directory naming looks a little weird. What is the subjects 
directory ? Are all your subjects (all cross, base and long of all 
subjects) in CT_10?
What is BLD013_  is that the name of the base (=subject template)?

Did you run the long_mris_slopes command (follow instructions here):
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel
(there is also some info about this in the longitudinal tutorial)

By the way, we usually recommend to do linear mixed effects modeling for 
longitudinal data. This is especially true if:
- different subjects have differently many time points
- the time deltas between time points vary quite a lot

Best, Martin

On 10/23/2015 10:09 AM, Wrobel, Pawel wrote:
> Hello Dear FreeSurfer Developers,
>
> Thank You once again for helping me a couple of months ago. Today I came 
> across a new obstacle, as I have been trying to analyse longitudinal material.
> I have performed all preparation steps and I started performing statistical 
> analysis in Qdec when receiving following message:
>
> Error in Analyze: Couldn't open 
> .../FreeSurfer_output/subjects/CT_10/BLD013_/surf/lh.thickness.fwhm15.fsaverage.mgz
>  or .mgh file.
>
> I have checked in the surface directory and I could not find this file. There 
> were several variations of it, but not a file with this particular name.
>
> I have been working with Freesurfer5.3.
>
> Thank You for Your help!
> Pawel
>
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>
>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] nifti1Read(): unsupported slice timing pattern 5 -- mri_convert fix?

[Alex Kell]

Hi,

I'm analyzing data from a collaborator who used SPM to generate some
niftis, and freesurfer is unable to read these.  I get the following error:
nifti1Read(): unsupported slice timing pattern 5

Someone previously

had the same problem that I currently have, and Doug sent them a modified
version of mri_convert.

Could you send me the modified version of mri_convert?


Thanks,
Alex
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Re: [Freesurfer] nifti1Read(): unsupported slice timing pattern 5 -- mri_convert fix?

[Douglas N Greve]

try this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert


On 10/23/2015 12:28 PM, Alex Kell wrote:
> Hi,
>
> I'm analyzing data from a collaborator who used SPM to generate some 
> niftis, and freesurfer is unable to read these. I get the following 
> error:
> nifti1Read(): unsupported slice timing pattern 5
>
> Someone previously 
>  
> had the same problem that I currently have, and Doug sent them a 
> modified version of mri_convert.
>
> Could you send me the modified version of mri_convert?
>
>
> Thanks,
> Alex
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Head circumference

[John Anderson]

Dear FS experts,

I want to inquire if there is any script in Freesurfer that can help to calculate the head circumference from MPRAGE ?

Thanks for any advice!

 

 
 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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[Freesurfer] Funcroi-Table-Sess Error

[Morenikeji Adebayo]

Hi there,

I ran the following analysis commands:

mri_cor2label --c 
/autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 11106 
--l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label
funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh -roi 
roiconfig_ACC_lh
funcroi-table-sess -analysis analysis_induc_block.lh -contrast 
contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o 
sumtable_ACC_lh.dat

After running the 'funcroi-table-sess’ command I got the following error:

ERROR: There is a vertex in the label that cannot be matched to the surface. 
This usually occurs when the label and surface are from different subjects or 
hemispheres of the surface has been changed since the label was created.

It seems that the problem might be that the command is using my participant (in 
this case, nmasa_001) as the source subject  BUT it’s using fsaverage as the 
target subject. I want the target subject to be my participant as well (not 
fsaverage).

Is there a way that I can specify the target subjects? Or is there a more 
efficient way do what I’m trying to do (ie: 1. generate labels for each 
participant based on their aparc+aseg file and 2. calculate the mean contrast 
signal from each ROI for each participant).


Thanks,
Keji



---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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Re: [Freesurfer] Help with V6

[Douglas Merkitch]

Hello Noah,

Could you be more specific as to how you were able to resolve this problem? 
What additional tweaks were necessary?

I too received the same error message:

ERROR: Flag -subfields-T1 unrecognized.
-all -s 1048_v6beta_hippsubfieldsT1 -subfields-T1
Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version 12.6.0: Wed 
Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Fri Oct 23 13:10:17 CDT 2015

I'm running freesurfer-Darwin-OSX-stable-v6-beta-20150921 on a mid 2012 MacPro 
(OS X 10.8.5). I also installed the Matlab runtime as instructed.

Any help would be greatly appreciated!

Thanks,

Doug

Doug Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu




Thanks Noah. It doea say on the website that you need the 2012b runtime, but
its definitely buried among too much other, less critical stuff
Cheers
E

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: 
www.bcbl.eu/legal-disclaimer


- Original Message -
From: Noah Markowitz http://gmail.com>>
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Sent: Sat, 04 Jul 2015 13:57:53 +0200 (CEST)
Subject: Re: [Freesurfer] Help with V6

Hey Eugenio,

I was able to resolve it with the help of another expert. One of the problems
definitely was that 2014b doesn’t run on the hippocampal-subfields module.
Maybe try adding that as a note to the website as numerous people have access
to the 2014b version and 2015a was just released. Thanks again for all the help.

Cheers,
Noah

> On Jul 3, 2015, at 5:12 PM, Eugenio Iglesias 
> http://bcbl.eu>> wrote:
>
> Hi Noah,
> this error is pretty weird. Can you please send us the exact command you
> executed?
> Regarding the runtime: your 2014b runtime won't work. You need to follow the
> instructions here:
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
> Cheers,
> Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: 
> www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Noah Markowitz" http://gmail.com>>
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, July 3, 2015 4:20:02 AM
> Subject: [Freesurfer] Help with V6
>
> Hi,
>
> I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the
> error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and
> source just as described for previous versions.
>
> Also, I have Matlab 2014b downloaded on the computer (obviously comes with
> runtime) but am unsure if the runtime folder needs to be placed in the FS
> folder or is fine where it is.
>
> Any FS experts help with these two problems and concerns? Much appreciated if
> you do.
>
> Cheers,
>
> Noah Markowitz
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Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

[Yun Wang]

Hi,

I recently using Freesurfer 6 beta version to recon high resolution data with 
the -cm flag, however,   the program exit with error.
total defect index = 0

\n mris_euler_number ../surf/rh.orig \n

Darwin AlbertStekiiMac 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 
PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64



recon-all -s HIP001_3d exited with ERRORS at Thu Oct 22 08:15:53 CDT 2015

Attached is the whole log history. 

Thanks for any idea!

Yun 

> On Oct 18, 2015, at 14:10, Bruce Fischl  wrote:
> 
> you can use the -cm flag, but you might want to try out a beta of v6 instead 
> of 5.3
> On Sun, 18 Oct 2015, Yun Wang wrote:
> 
>> Glad to hear this ! So how should I specify high resolution structure using 
>> recon-all command?
>> 
>> 
>>> On Oct 17, 2015, at 10:09, Bruce Fischl  wrote:
>>> 
>>> High resolution fMRI has always been supported. V6 beta has better support 
>>> for high-resolution structurals. If your fMRI is higher than 1mm isotropic 
>>> then having higher res structurals (and hence denser cortical meshes) might 
>>> be useful
>>> 
>>> cheers
>>> Bruce
>>> 
>>> 
>>> 
>>> On Sat, 17 Oct 2015, Yun Wang wrote:
>>> 
 Can the recon-all for high resolution fMRI data be used in V6 beta 
 freesurfer now? If
 so, how to use it?
 
 On Jun 25, 2015, at 13:36, Allison Moreau 
 
 wrote:
 Hi Falk and Thomas,
 We are actually working on testing the -hires flag now for the v6 release. 
 We
 intend to release it with v6.
 -Allison
 On 06/25/2015 07:09 AM, Falk Lüsebrink wrote:
 Hi Thomas,
 
 this looks like a really nice script and a lot better than my own. In the
 upcoming release of FreeSurfer v.6 my work-around probably is not needed
 anymore. However, I haven’t been able to have a look at the dev release yet
 and whether the standard recon-all features a flag to process high
 resolution data.
 
 Best,
 Falk
 
 P.S. Following your instructions one will definitely become a coffee
 junkie. :D
 
 Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 [mailto:freesurfer-boun...@nmr.mgh.harvard
 .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY)
 Gesendet: Mittwoch, 24. Juni 2015 14:35
 An: freesurfer@nmr.mgh.harvard.edu
 Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
 
 Hello!
 
 I wrote a bash script some time ago to process data acquired at a
 sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink
 (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might
 be helpful for others, too, as there are some questions about it in the
 mailing list archives, so here it
 is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy
 about any comments!
 
 Best,
 Thomas
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>>> 
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>> 
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