Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

[Dianne Patterson]

Since I'm following the example on the github page, using the ds005
dataset, now with the correct license binding, I am surprised to see
freesurfer exiting with errors (but I don't know much about freesurfer):

I run this:

docker run -ti --rm -v
/Volumes/Main/Working/BIDS_TESTING/license.txt:/license.txt:ro -v
/Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v
/Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
/bids_dataset /outputs participant --participant_label 01 02 --license_file
/license.txt

A few hours later: recon-all -s sub-01 exited with ERRORS at Sun Feb  4
03:27:11 UTC 2018
And then sub-02 does not run

Is this what I should expect?

Thanks,

Dianne

On Mon, Jan 22, 2018 at 9:54 PM, Dianne Patterson 
wrote:

> Wonderful...and makes total sense!  Thankyou...it is off and running now.
> -Dianne
>
>
> On Mon, Jan 22, 2018 at 8:19 PM, Chris Gorgolewski <
> krzysztof.gorgolew...@gmail.com> wrote:
>
>> Hi Dianne,
>>
>> You need to "mount" the using -v the same way input and output
>> directories are mounted. For example:
>>
>> docker run -ti --rm -v /Volumes/Main/Working/BIDS_
>> TESTING/license.txt:/license.txt:ro -v 
>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>> /bids_dataset /outputs participant --license_file /license.txt
>>
>> Best,
>> Chris
>>
>> On Mon, Jan 22, 2018 at 7:13 PM, Dianne Patterson 
>> wrote:
>>
>>> Dear All,
>>>
>>> After trying the example bids app (which worked fine), I am trying the
>>> freesurfer bids app. I have built the docker container on my mac and I have
>>> the ds005 data directory here and the license.txt which I requested from
>>> freesurfer.
>>> I asked for a linux license (assuming the container contains linux and
>>> that was the relevant fact).
>>>
>>> dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v
>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v
>>> /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>> /bids_dataset /outputs participant --license_file "license.txt"
>>> 1: You should define 'SliceTiming' for this file. If you don't provide
>>> this information slice time correction will not be possible. (code: 13 -
>>> SLICE_TIMING_NOT_DEFINED)
>>> /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
>>> /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
>>> /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
>>> /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz
>>> /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz
>>> /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz
>>> /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz
>>> /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz
>>> /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz
>>> /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz
>>> ... and 38 more files having this issue (Use --verbose to see them all).
>>>
>>> Summary: Available Tasks:  Available
>>> Modalities:
>>> 133 Files, 1.77GBmixed-gambles taskT1w
>>> 16 - Subjects  inplaneT2
>>> 1 - Sessionbold
>>>
>>>
>>> Traceback (most recent call last):
>>>   File "/run.py", line 165, in 
>>> raise Exception("Provided license file does not exist")
>>> *Exception: Provided license file does not exist*
>>> ===
>>> If I provide the full path to the license file, it still fails:
>>>
>>> docker run -ti --rm -v 
>>> /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro
>>> -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
>>> /bids_dataset /outputs participant --license_file
>>> "/Volumes/Main/Working/BIDS_TESTING/license.txt"
>>>
>>> Suggestions?  How do I tell freesurfer where the license file is?
>>>
>>> Thanks so much,
>>>
>>> Dianne
>>>
>>>
>>>
>>> --
>>> Dianne Patterson, Ph.D.
>>> Research Scientist
>>> d...@email.arizona.edu 
>>> or
>>> dianne...@gmail.com
>>> University of Arizona
>>> Speech and Hearing Science 314
>>> 1131 E 2nd Street, Building #71
>>> 
>>> (Just East of Harvill)
>>> ==
>>> If you don't hear back from me (and you expected to),
>>> I blame the University's new SPAM filter.
>>> Please write to my gmail account.
>>> ==
>>> Antipiphany: That moment when you realize how little you actually know
>>> ==
>>>
>>> --
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>>> Groups "bids-discussion" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
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Re: [Freesurfer] Recon-all -nonuintensitycor

[Douglas Greve]

I don't think so


On 2/3/18 3:28 PM, Alexis Moscoso wrote:
Thanks Douglas. Just one more quick question: will -nonuintensitycor 
work if I set the -3T flag? As far as I know, -3T changes some 
parameters of the N3 correction and makes use of Schwarz atlas. I was 
wondering whether this flag interferes with -nonuintensitycor.


El El sáb, 3 feb 2018 a las 21:01, Douglas Greve 
> escribió:


If you want to just run the recon-all pipeline without using n3,
you'll have to do something else. You can copy orig.mgz to nu.mgz
(or create a symbolic link, which is probably better), then run
with -nonuintensitycor


On 1/29/18 7:14 PM, Alexis Moscoso wrote:

Hello Freesurfer developers,

I’m trying to run a recon-all on ADNI T1 images. Since these data
have already been corrected with the N3 correction, I want to
turn off N3 correction in the recon-all process so I added
-nonuintensitycor after -all. However, when I run it, I get an
error during the normalization step since it no nu.mgz file is
generated and cannot be found by mri_normalize. I’d like to know
how to do the everything except the N3 correction.

1) Freesurfer version: 6.0.0


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Re: [Freesurfer] Recon-all -nonuintensitycor

[Alexis Moscoso]

Thanks Douglas. Just one more quick question: will -nonuintensitycor work
if I set the -3T flag? As far as I know, -3T changes some parameters of the
N3 correction and makes use of Schwarz atlas. I was wondering whether this
flag interferes with -nonuintensitycor.

El El sáb, 3 feb 2018 a las 21:01, Douglas Greve 
escribió:

> If you want to just run the recon-all pipeline without using n3, you'll
> have to do something else. You can copy orig.mgz to nu.mgz (or create a
> symbolic link, which is probably better), then run with -nonuintensitycor
>
> On 1/29/18 7:14 PM, Alexis Moscoso wrote:
>
> Hello Freesurfer developers,
>
> I’m trying to run a recon-all on ADNI T1 images. Since these data have
> already been corrected with the N3 correction, I want to turn off N3
> correction in the recon-all process so I added -nonuintensitycor after
> -all. However, when I run it, I get an error during the normalization step
> since it no nu.mgz file is generated and cannot be found by mri_normalize.
> I’d like to know how to do the everything except the N3 correction.
>
> 1) Freesurfer version: 6.0.0
>
>
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Re: [Freesurfer] aparcstat2table with new destrieux atlas

[Douglas Greve]

It should be possible. Just specify the annotation you want to use iwth 
the -p flag (run with -help to get more info)



On 1/25/18 12:48 PM, Lisa Delalande wrote:

Dear FreeSurfer expert,

I would like to use the new destrieux atlas for extracting anatomical 
data with the aparcstat2table command. Is that possible ? If yes can 
you give me the command ? Or give me some references that can help me ?



Thanks in advance
Best regards

Lisa


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Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug,

I have uploaded the files you requested. Thank you for your help.

Best,
Paul

On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve 
wrote:

> Can you upload the glmfit folders and the glmfit input (--y file) to our
> filedrop?
>
> https://gate.nmr.mgh.harvard.edu/filedrop2/
>
> On 2/1/18 7:46 PM, miracle ozzoude wrote:
>
> Hello Doug,
>
> I have attached a screen shot of the mask.mgh for both right and left
> hemispheres. Everything looks yellow. I followed the paired t-test tutorial
> on the wiki page (included my scripts, fsgd files, and matrix in email
> thread). How do i go about fixing it? Thanks you
>
> Best,
> Paul
>
> On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve 
> wrote:
>
>> that usually means that something has gone wrong with the analysis. Do
>> the maps look ok? In particular, look at the mask
>>
>>
>>
>> On 1/20/18 1:56 PM, miracle ozzoude wrote:
>>
>> Hello Doug,
>>
>> I tried using the MC tables that FS distributed. However, i got an error
>> about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
>> fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and
>> cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3
>> on mac. Thank you.
>>
>> Best,
>> Paul
>>
>> mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos
>> --cwpvalthresh 0.05 --2spaces --overwrite
>> mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
>> --cwpvalthresh 0.05 --2spaces --overwrite
>>
>> On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve > > wrote:
>>
>>> Why are you doing your own MC simulation? You can just use the tables
>>> that we distribute ...
>>>
>>> On 1/17/18 6:12 PM, miracle ozzoude wrote:
>>>
>>> Hello Experts,
>>>
>>> I am running a paired t-test cortical thickness analysis based on the
>>> instruction on the wiki page (https://surfer.nmr.mgh.harvar
>>> d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't
>>> not created when i corrected for multiple comparisons. Below are my script,
>>> fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z
>>> maps. Please can you help me figure out why the error is happening. Thank
>>> you.
>>>
>>> Best,
>>> Paul
>>>
>>> *Script*:
>>> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
>>> martrix2=age.mtx
>>> #resample each subjects's left and right hemisphere data to fsavarage.
>>> mris_preproc --target fsaverage --hemi lh --meas thickness --out
>>> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>>> mris_preproc --target fsaverage --hemi rh --meas thickness --out
>>> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>>> # #smoothen the concatenated file by 5mm FWHM. --cortex means only
>>> smooth areas in the cortex. N:B. FWHM changes based on study type.
>>> mri_surf2surf --hemi lh --s fsaverage --sval
>>> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
>>> lh.paired-diff.thickness.sm05.mgh
>>> mri_surf2surf --hemi rh --s fsaverage --sval
>>> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
>>> rh.paired-diff.thickness.sm05.mgh
>>> # #Run GLM analysis
>>> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
>>> $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
>>> lh.paired-diff.glmdirir
>>> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
>>> $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
>>> rh.paired-diff.glmdir
>>> # # #Run Clusterwise correction for multiple comparisons using MONTE
>>> CARLO. First create a table for of simulations
>>> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
>>> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
>>> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
>>> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
>>> *Fsgd file 1:pairs.fsgd*
>>>
>>> GroupDescriptorFile 1
>>>
>>> Class ADEX
>>>
>>> Input 1000_1 ADEX
>>>
>>> Input 1000_2 ADEX
>>>
>>> Input 1001_1 ADEX
>>>
>>> Input 1001_2 ADEX
>>>
>>> Input 1003_1 ADEX
>>>
>>> Input 1003_2 ADEX
>>>
>>> Input 1005_1 ADEX
>>>
>>> Input 1005_2 ADEX
>>>
>>> Input 1008_1 ADEX
>>>
>>> Input 1008_2 ADEX
>>>
>>> Input 1013_1 ADEX
>>>
>>> Input 1013_2 ADEX
>>>
>>> Input 1014_1 ADEX
>>>
>>> Input 1014_2 ADEX
>>> *Fsgd file 2: paired_diff.fsgd*
>>>
>>> GroupDescriptorFile 1
>>>
>>> Class ADEX
>>>
>>> Variables Age
>>>
>>> Input 1000 ADEX 72
>>>
>>> Input 1001 ADEX 76
>>>
>>> Input 1003 ADEX 72
>>>
>>> Input 1005 ADEX 80
>>>
>>> Input 1008 ADEX 72
>>>
>>> Input 1013 ADEX 80
>>>
>>> Input 1014 ADEX 80
>>>
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Re: [Freesurfer] FSFAST

[Douglas Greve]

That file should be in the same dimensions, no?


On 1/30/18 12:19 AM, Ashley Cole wrote:
I just noticed that that file "fmc.odd.sm5.nii.gz" is created after 
selxavg3-sess. I was wondering how can I preprocess the functional 
image and have the output with the same dimension as the f.nii.gz 
without performing any contrasts. I just need to look at the signal in 
some ROIs without performing any contrasts. I hope this makes sense.


Thanks,
Ash

On Mon, Jan 29, 2018 at 10:54 PM, Ashley Cole > wrote:


Hello,

I have several nifti files. I have preprocessed some of them
before. I used this command:
preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh
-mni305 -fwhm 5 -per-session -force

The output files contained fmc.odd.sm5.self.lh.nii.gz,
fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and
*fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was
the file that I needed for my further analyses. However, when I
run the same command on another nifti file which was obtained from
the same scanner and the same session, the output doesn't have the
fmc.odd.sm5.nii.gz.

I ran it several times but it never gave me that file. Also, it
doesn't give me any errors.

I appreciate any help.

Ash




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Re: [Freesurfer] Recon-all -nonuintensitycor

[Douglas Greve]

If you want to just run the recon-all pipeline without using n3, you'll 
have to do something else. You can copy orig.mgz to nu.mgz (or create a 
symbolic link, which is probably better), then run with -nonuintensitycor



On 1/29/18 7:14 PM, Alexis Moscoso wrote:

Hello Freesurfer developers,

I’m trying to run a recon-all on ADNI T1 images. Since these data have 
already been corrected with the N3 correction, I want to turn off N3 
correction in the recon-all process so I added -nonuintensitycor after 
-all. However, when I run it, I get an error during the normalization 
step since it no nu.mgz file is generated and cannot be found by 
mri_normalize. I’d like to know how to do the everything except the N3 
correction.


1) Freesurfer version: 6.0.0


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Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume mask to the surface space for mri_mcsim using my own template?

[Douglas Greve]

You need to map the mask into the fsaverage space. Probably the easiest 
way to do this is to run recon-all on your template to get surfaces. 
Then run mri_vol2surf to map your mask onto the surface, then use 
mris_apply_reg to map your surface mask to fsaverage (make sure to 
--no-rev since you are mapping a mask). If you want to do FDR, then run 
mri_fdr.


On 1/29/18 12:17 PM, Charlotte Grosse Wiesmann wrote:
> Dear freesurfer experts,
>
> I would like to restrict my surface analyses (cortical thickness and surface 
> area) to a mask from an fMRI meta-analysis using my own subject-specific 
> template that I created with ANTS. So far, I have used Qdec and wanted to 
> correct for cluster size running the Monte Carlo (MC) simulation on my own 
> template.
> Now I would like to restrict the simulation to my mask to do a small volume 
> correction in my regions of interest. I mapped the mask to my own template 
> (in volume space) using ANTS (WarpImageMultiTransform) but how can I get this 
> mask to the surface space to run the MC simulation on my own template within 
> this mask?
>
> I was planning to do:
> mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z 
> --surface my_template ?h --nreps 1 --mask mymask.mgz
>
> How do I get mymask.mgz in the correct space for this?
>
> And can I continue using Qdec or do I have to use glmfit for these analyses?
>
> In addition: is it also possible to do a small volume correction using FDR 
> rather than cluster-size correction?
>
> Thanks for your help!
>
> Charlotte
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Re: [Freesurfer] # voxels above thresholds across aparc+aseg regions - mri_segstats?

[Douglas Greve]

Hi Sara, it looks like you are doing a functional constraint. See these 
slides


http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part2.pptx 

(tutorial here 
https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0)

and let me know if  you have any questions
doug

On 1/29/18 11:33 AM, Makaretz, Sara Johanna wrote:


Hi FS group,


My goal is to calculate the % of voxels in a given region that are 
higher than a region-specific threshold. This is what I've done so far 
for each subject:



  * recon T1
  * coregister vol.nii to T1
  * move aparc+aseg.mgz into functional space
  * mri_segstats --i vol.nii --seg aparc+aseg.functionalspace.nii
--sum vol.aparc+aseg.stats to get NVoxels & mean stats


For each subject, for each cortical region (Seg1001-1035 & 
Seg2001-2035), I now want to count the number of voxels that are above 
region-specific thresholds as found in thresh.lst, ie.



  ctx-lh-bankssts    Seg1001    1.383697722
  ctx-lh-caudalanteriorcingulate    Seg1002    1.272858762
  ctx-lh-caudalmiddlefrontal    Seg1003    1.167540497
  ...

Do you have any advice on the best way to do this? I think I can use 
mri_segstats, but am not sure if I'm looking at the right arguments 
and/or if there is a more straightforward way to do this. This is what 
I have so far:



  foreach s (`cat s.lst`)   /   foreach seg (`cat thresh.lst | awk 
'{print $2}'`)


  set thresh = `cat thresh.lst | grep $seg | awk '{print $3}'`

  mri_segstats --i vol.nii --seg aparc+aseg.functionalspace.nii --id 
$seg --maskthresh $thresh --masksign pos --sum tmp.$seg.stats


  ...and then grep NVoxels from tmp.$seg.stats, grep total NVoxels 
from vol.aparc+aseg.stats, divide/echo into summary stats file?




Thank you in advance for any advice!


Best,

Sara




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Re: [Freesurfer] Misalignment between functional and anatomical data with bbregister

[Douglas Greve]

what version of FS are you using? What is your bbregister command line? 
You should not smooth the data before alignment (usually you would use 
the template used for MC). You should also make sure that the 
deobliquing does not mess up the geometry info in the nifti file. Load 
the template file into freeview and make sure that it is aligned 
properly. Definitely do not convert it into MNI space.



On 1/26/18 5:50 PM, Rachel Bencic wrote:

Dear Freesurfer Team,

I am an image processing novice and am trying to register 
resting-state data to an anatomical scan using bbregister. The T1s 
have been run through Freesurfer's reconall pipeline, and the EPIs 
have undergone the following preprocessing steps:

- slice time correctoin
- deobliquing
- drop first few images
- motion correction / volume registration
- despike
- temporal filter
- smoothing
(I tried registering EPIs that had been aligned to MNI space to the 
anatomicals, with similar outcomes.)


Ultimately, I plan to use Freesurfer-generated ROIs (those from Yeo et 
al., 2011), based on the anatomical scan, to run graph theory analyses 
on the resting-state data.



However, when I use bbregister, the files are grossly misaligned. 
Below is an image of the EPI file on top of the white matter surface 
(in green). You can see that the EPI file looks very large.




Has anyone encountered this problem / does anyone have any suggestions 
as to what I might be doing wrong? Any help would be greatly appreciated.


Thank you in advance for your time.


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Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

[Douglas Greve]

Strange. Can you send me the analysis.info file?


On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
> Hello Dr. Greve,
>
> Yes it exists. The output below was with debug option.
>
> Best
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, January 30, 2018 8:40 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> Does the file 
> /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If 
> so, can you run it with -debug as the first option and send the terminal 
> output?
>
> On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
>
>
> Hello FreeSurfer experts,
>
> I am getting this strange error when running selxavg3-sess. (in selxavg3 
> command I am calling the analysis file with: -a rtopyTR2.rh) When the system 
> enters fast_selxavg3, it cannot read analysis.info, thus produces the 
> following output:
>
> #@# Sess05 ###
> /home/vm01/local/freesurfer/Project_bold/Sess05
> -
> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> -
> outtop = /home/vm01/local/freesurfer/Project_bold
> Extension format = nii.gz
> ERROR: could not open rtopyTR2.rh/analysis.info
> else
> else
> echo "--" | tee -a $LF
> echo --
> tee -a 
> /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
> --
> rm $MLF
> rm /tmp/selxavg3-sess-10173.m
> if ( ! -e $okfile ) then
> if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
> echo "ERROR: fast_selxavg3() failed\n" ;
> echo ERROR: fast_selxavg3() failed\n
> ERROR: fast_selxavg3() failed\n
> exit 1 ;
> exit 1
>
> The analysis folder it is referring to( rtopyTR2.rh) is in the directory from 
> which I am calling selxavg3-sess. It has the analysis.info file in which 
> doesn't have any restrictions. To troubleshoot, I moved the folder to inside 
> the session's functional directory and inside the session folder and these 
> didn't create any changes. I looked at the script and tried to debug there 
> but didn't give any results. It gave a similar error when trying to open the 
> config file of contrast in mkcontrast-sess. (I also don't have root 
> access)Any help is appreciated!
>
> Best,
> Idil
>
>
>
>
>
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Re: [Freesurfer] funcroi-table-sess: how to specify frames for multi-band data

[Douglas Greve]

Hi Keishi,

the frame parameter is the frame in the contrast file. Most of the time 
this file will only have one frame (-frame 0) unless you have specified 
a multivariate contrast. This does not have anything to do with 
multiband. What is your intention when looping through from 0 to 19?

doug


On 1/28/18 11:41 PM, Keishi NOMURA wrote:
> Hi all,
>
> I’m using : freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> I’d like to plot HRF for each condition for each subject, using data acquired 
> by multi-band EPI.
> Here are the commands I used:
>
>
> funcroi-config -roi rh.V1.roicfg -label rh.V1.label -analysis RH_fwhm8 -force
> funcroi-sess -s ORI01 -roi rh.V1.roicfg -df sessdirfile
>
> # m: frames
>
> foreach m ( 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 )
>funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis 
> RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt 
> -frame $m
> end
>
>
> Then I got an error like “Error: input frame = 2, input volume only has 1 
> frames”.
>
> I referred to the related questions:
>https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15883.html
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017958.html
> It seems that there is nothing wrong with these commands, except for 
> specifying the frames.
> One possibility is that using multi-band data is somehow causing trouble.
> I’m now using multi-band factor = 8 and TR = 0.8 sec, so then I set the 
> frames to multiple number of TR = 0.8, and ran the commands again:
>
>
> foreach m ( 0.8 1.6 2.4 3.2 4.0 4.8 5.6 6.4 7.2 8.0 8.8 9.6 10.4 11.2 12.0 
> 12.8 13.6 14.4 15.2 16 )
>funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis 
> RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt 
> -frame $m
> end
>
>
> But still I get errors like “Error: input frame = 2, input volume only has 1 
> frames”. (when I used frame = 2.4. Hence, it seems that we cannot use 
> non-integral inputs)
> So, my question is:
> (1) How should I specify frames when I use multi-band data?
> (2) Regarding (1), what temporal resolution do I get when I use TR = 0.8? 
> (for example, TER = 0.8/20 = 0.04 or anything like that)
> (3) Or, is there anything wrong with my commands other than frames?
>
> Thank you,
> Keishi
>
>
>
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Re: [Freesurfer] How to extract stats of the regions that is covered by large clusters

[Douglas Greve]

what do you mean by stats? The mean values of the inputs for each 
cluster and subject will be in the output ("ocd" file). See 
mri_glmfit-sim --help



On 1/31/18 4:48 PM, Shatil, Anwar Shahadat wrote:


Hello Experts:

After running mri_glmfit sim, I got below clusters:

ClusterNo  Max VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ    CWP    
CWPLow CWPHi   NVtxs    WghtVtx   Annot


   1   16.567 56197  13752.71    -36.8  -15.5   55.0  0.00020  
0.0 0.00040  30900   180209.80  precentral


   2    9.630 57862   3018.98    -29.7  -72.0  -10.1  0.00020  
0.0 0.00040   4620    23119.05  fusiform


   3    9.488 162470   2465.82    -16.0  -79.3    7.4  0.00020  
0.0 0.00040   4108    19097.47  pericalcarine


   4    8.845 35506   1860.62    -24.5  -79.0   23.1  0.00020  
0.0 0.00040   3375    15122.28  superiorparietal


   5    6.223 84246   1019.33 -4.8   15.4   -6.3  0.00020  
0.0 0.00040   1760 6950.26  rostralanteriorcingulate


However, Cluster-1 area is large compared to others and it actually 
postcentral, and some portion of paracentral region. How can I extract 
the stats for these regions?


Thanks,

Anwar


Anwar S. Shatil

Research Assistant, Medical Imaging
Sunnybrook Health Sciences Centre
Toronto, ON, M4N 3M5
Email: anwar.sha...@sunnybrook.ca 

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Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm

[Douglas Greve]

Can you send the terminal output of one of the runs that fails?


On 1/31/18 4:10 PM, Sims, Sara A wrote:


Freesurfers,

I am trying to use a cortical label to label wm. I am using the 
following command line:


mri_aparc2aseg --s $patient --annot 8V1 –labelwm

And most of the time in most subjects this works, however sometimes 
the output file doesn’t label any wm with the 3000+N or 4000+N like it 
usually does. I have tried changing the -wmparc-dmax, -hypo-as-wm, 
-smooth_normals. Basically everything I could find but it won’t budge 
even though doing other labels in the same person works fine. Fyi: The 
original cortical label is also correctly place in the cortical ribbon.


Any ideas?

Please!

Thanks,

Sara Sims

Graduate Research Fellow

University of Alabama at Birmingham

Department of Psychology

205-975-4060

sno...@uab.edu



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Re: [Freesurfer] Spatial smoothing during preprocessing

[Douglas Greve]

On 1/31/18 8:33 PM, Ben Smith wrote:

Hi all,

I read from the freesurfer discussion archives that when combining FSL 
FEAT with freesurfer, one should definitely NOT do spatial smoothing 
in the preprocessing when preparing to examine cortical data.


https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11536.html

However I can see that in the FSFast pipeline, 2D and 3D smoothing 
*/is*/ included in the FSFast preprocessing.


So:

 1. I am guessing that the 2D smoothing applies only to the surface
and is smoothing on the surface space. Is this correct?


Yes


 1. I'm also guessing that the 3D smoothing applies only to the
subcortical regions. Is all this also correct?


Yes


 1. The freesurfer.feat.ppt guide does NOT contain any instructions
for doing any smoothing on data derived from FSL. But I assume
that, if smoothing is done during FSFast preprocessing but is not
done when preprocessing in FSL, then smoothing will still need to
be done at a subsequent point with the FSL data. But I don't see
instructions on that in the Freesurfer FEAT documentation on
freesurfer.feat.ppt. If I do FSL preprocessing+1st-level analysis
with no spatial smoothing, and then proceed with the analysis, at
which point do I apply preprocessing? Is there a guide
specifically describing how to apply smoothing to data originating
from FSL?

You can apply it after concatenate the surface overlays together. Use 
mri_surf2surf or mris_fwhm

Thank you very much to anyone willing to help!

Best regards

Ben
___
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w | +1 213-740 7851
m | +1 323-385 9349
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Re: [Freesurfer] Problems transforming T1 to talairach

[Douglas Greve]

Try adding -oc 0 0 0 to the mri_convert command line


On 2/2/18 7:27 AM, Helen Beaumont wrote:
> I am using the command
> mri_convert -at transforms/talairach.xfm  brain.mgz brain_in_tal.nii.gz
>
> to convert a native-space skull-stripped T1 image to talairach space. I used 
> recon-all to generate the transform matrix, and the segmentation and 
> everything look good. But the T1_in_talairach image is not good - the brains 
> are ending up different sizes, and frequently have the posterior chopped off.
> Please what am I doing wrong? Should I be applying the inverse of the 
> transform?
>
> Helen Beaumont PhD
> University of Manchester
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Re: [Freesurfer] Group and ROI analyses in qdec

[Douglas Greve]

On 2/2/18 8:01 AM, Backhausen, Lea wrote:

Dear freesurfer experts,
I started using qdec for comparing cortical measures in adolescent 
patients with ADHD versus typically developing adolescents and I have 
a few questions concerning the ROI analysis as well as the 
Desikan-Killiany versus Destrieux atlas.
English is not my native language so please excuse typing errors or 
wrong expressions.
1)Is it somehow possible to have the significant clusters mapped onto 
the Destrieux atlas in qdec instead of the Desikan-Killiany one?
Sorry, I don't know. No one is currently "in charge" of qdec, so we 
don't support it all that well. I think you can select the annotation 
though.


2)I would like to export the mean thickness/surface area from 
significant clusters to SPSS to correlate them with clinical symptoms. 
I understand you can either use means from the stats tables 
(aparc_thikness_lh.txt etc.) or manually draw a ROI and then map the 
lable back to other subjects. But is there also a way to simply export 
the measures from the significant clusters that show up without 
drawing around them or export measures from the peak vertices?

No, I would do your analysis using the "command-line stream".


3)If I use methods as described in 2), do I have to be concerned about 
‘double dipping’ or ‘circular analysis’?
Possibly so, unless your post hoc tests are completely independent of 
the test used to generate the clusters.


4)Does the measure ‘area.pial’ you can select during design creation 
correspond to ‘cortical surface area’ and the measure ‘area’ to ‘WM 
surface area’? W

Yes
hich measure do the aparc_area_lh.txt files that I get when generating 
stats data tables correspond to? I do not see aparc_area.pial.txt 
files, should I be getting them?
It refers to the white surface. Not sure where you are getting these 
files from, but you can generate the pial area.


5)After reading a lot about correcting for global brain measures I am 
still confused about the best way to do it. I am quite sure that for 
the volume-based measures it is best to control for ICV/eTIV but for 
thickness and surface area I read different approaches from not 
controling to using total brain volume, global thickness or ICV. Is it 
safe not to control for anything for thickness measures as I do not 
expect any kind of atrophy in my sample? What should my decision be 
based on?
In general, you do not need to control for any global measure with 
thickness since thickness does not change with head or  brain size.


Sorry, these are many questions – I appreciate any thoughts on these 
problems, thank you so much!


Lea Backhausen, B.Sc.

Research Assistant
Department of Child and Adolescent Psychiatry, Faculty of Medicine of 
the Technische Universität Dresden, Dresden, Germany







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Re: [Freesurfer] One Group (One Factor), Two Covariates

[Douglas Greve]

On 2/2/18 7:47 AM, std...@virgilio.it wrote:


Hi list,

in reference to One Group (One Factor), Two Covariates

https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx

that has been applied on FS-FAST fcMRI data

I obtain three folder, respectively, for "main", "covariate 1", 
"covariate 2".


What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
each folder?

Please correct my conclusions if they are wrong.

1 - In the "Main" folder, the sig.nii.gz contains the results of 
One-sample t test regressing out the effect of the two covariates.



Correct


2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 1 
regressing out the effect for the covariate 2.



Yes (and the main)


3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 2 
regressing out the effect for the covariate 1.



Yes (and regressing out the main)


Thanks


Stefano

*
*

*
*



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Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

[Douglas Greve]

Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search 
through the mail archives for an example on how to use it



On 2/3/18 12:10 PM, std...@virgilio.it wrote:


Hi list,

Is there a way to obtain a map that report the "vertex by vertex" 
correlation between the FC (obtained by FS-FAST) and cortical thickness?


Thanks


Stefano



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Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[Douglas Greve]

Can you upload the glmfit folders and the glmfit input (--y file) to our 
filedrop?


https://gate.nmr.mgh.harvard.edu/filedrop2/


On 2/1/18 7:46 PM, miracle ozzoude wrote:

Hello Doug,

I have attached a screen shot of the mask.mgh for both right and left 
hemispheres. Everything looks yellow. I followed the paired t-test 
tutorial on the wiki page (included my scripts, fsgd files, and matrix 
in email thread). How do i go about fixing it? Thanks you


Best,
Paul

On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve 
> wrote:


that usually means that something has gone wrong with the
analysis. Do the maps look ok? In particular, look at the mask



On 1/20/18 1:56 PM, miracle ozzoude wrote:

Hello Doug,

I tried using the MC tables that FS distributed. However, i got
an error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I
checked and there's no fwhm00, the table starts from fwhm01 to
fwhm30. Below are my script and cache.mri_glmfi-sim.log files. My
FreeSurfer version is stable version 5.3 on mac. Thank you.

Best,
Paul

mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3
pos --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3
pos --cwpvalthresh 0.05 --2spaces --overwrite

On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve
> wrote:

Why are you doing your own MC simulation? You can just use
the tables that we distribute ...


On 1/17/18 6:12 PM, miracle ozzoude wrote:

Hello Experts,

I am running a paired t-test cortical thickness analysis
based on the instruction on the wiki page
(https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
).
However, the monte carlo files weren't not created when i
corrected for multiple comparisons. Below are my script,
fsgd files, mc-z log file, and a screenshot of contrast
folder missing mc.z maps. Please can you help me figure out
why the error is happening. Thank you.

Best,
Paul

*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
martrix2=age.mtx
#resample each subjects's left and right hemisphere data to
fsavarage.
mris_preproc --target fsaverage --hemi lh --meas thickness
--out lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas thickness
--out rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex
means only smooth areas in the cortex. N:B. FWHM changes
based on study type.
mri_surf2surf --hemi lh --s fsaverage --sval
lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval
rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
rh.paired-diff.thickness.sm05.mgh
# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd
$paired --C $martrix1 --C $martrix2 --surf fsaverage lh
--cortex --glmdir lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd
$paired --C $martrix1 --C $martrix2 --surf fsaverage rh
--cortex --glmdir rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple comparisons
using MONTE CARLO. First create a table for of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z
1 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05
--2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z
1 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05
--2spaces --overwrite
*Fsgd file 1:pairs.fsgd*

GroupDescriptorFile 1

Class ADEX

Input 1000_1 ADEX

Input 1000_2 ADEX

Input 1001_1 ADEX

Input 1001_2 ADEX

Input 1003_1 ADEX

Input 1003_2 ADEX

Input 1005_1 ADEX

Input 1005_2 ADEX

Input 1008_1 ADEX

Input 1008_2 ADEX

Input 1013_1 ADEX

Input 1013_2 ADEX

Input 1014_1 ADEX

Input 1014_2 ADEX

*Fsgd file 2: paired_diff.fsgd*

GroupDescriptorFile 1

Class ADEX

Variables Age

Input 1000 ADEX 72

Input 1001 ADEX 76

Input 1003 ADEX 72

Input 1005 ADEX 80

Input 1008 ADEX 72

Input 1013 ADEX 80

Input 1014 ADEX 80

Re: [Freesurfer] White matter hypointensities

[Douglas Greve]

Probably just partial volume correction


On 2/1/18 3:37 PM, Maksimovskiy, Arkadiy wrote:


Dear Experts,

I was wondering if anyone might know why the WM hypointensities total 
number in aseg does not match the sum of left and right white matter 
hypointensities.


Thanks,

Arkadiy

--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School



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Re: [Freesurfer] talaraich transformation error

[Douglas Greve]

Check and, if necessary, edit the transform.  Then re-run recon-all 
including the -no-tal-check option



On 2/2/18 9:14 AM, Dijkshoorn, A.B.C. (Aicha) wrote:

Hello free surfer developers,


I am attempting to compute cortical thickness for anatomical ROIs in 
neonates, but for some of my subjects I get the following error when I 
run the auto-recon1 command:




\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

Darwin leia.ds.umcutrecht.nl 14.5.0 Darwin Kernel Version 14.5.0: Sun 
Jun  4 21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64


recon-all -s N192_con_recon exited with ERRORS at Fri Feb  2 12:32:02 
CET 2018




Is there any way I can work around this error?


Kind regards,
Aicha Dijkshoorn



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[Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

[stdp82]

Hi list,

Is there a way to obtain a map that report the "vertex by vertex" correlation 
between the FC (obtained by FS-FAST) and cortical thickness?

Thanks


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