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Today's Topics:
1. Re: HCP_1200 parcellation problems (Greve, Douglas N.,Ph.D.)
2. Re: need assistance to decode QDEC results
(Greve, Douglas N.,Ph.D.)
3. Re: Cortical thickness volume ROI to surface {Disarmed}
(Greve, Douglas N.,Ph.D.)
4. Re: Error in selxavg3-sess (Greve, Douglas N.,Ph.D.)
5. Re: cannot find freesurfer/average/RB_all_2008-03-26.gca with
-use-gpu in v5.3 (Greve, Douglas N.,Ph.D.)
6. Re: cannot find freesurfer/average/RB_all_2008-03-26.gca with
-use-gpu in v5.3 {Disarmed} (Caspar M. Schwiedrzik)
7. Re: group analyses {Disarmed} (Greve, Douglas N.,Ph.D.)
----------------------------------------------------------------------
Message: 1
Date: Thu, 17 Dec 2020 14:28:37 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP_1200 parcellation problems
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <786b64c3-2d99-06ed-2fe3-812225238514@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Sorry, I can't tell from your email what the problem is. Can you elaborate?
On 12/9/2020 2:30 PM, najme soleimani wrote:
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Dear FreeSurfer Developers,
I downloaded the HCP_1200 subjects' structural extended data. I am attempting to have equal sized parcellation on scale 100, so I used parcellation results of Desikan atlas and increased the parcels from 68 to 100.
after obtaining split file, I run the following commands on FreeSurfer:
mris_divide_parcellation subj lh aparc.annot splitfile Desikan100
mris_divide_parcellation subj rh aparc.annot splitfile Desikan100
mri_aparc2aseg --s subj --annot Desikan100 --old-ribbon --o $SUBJECTS_DIR/subj/mri/Desikan100.subj.mgz
The interesting part is that after running this command some disconnectivity were seen in the parcels as it is shown in the picture. In 3D view, also, when the parcels were loaded on dsi studio, there were some holes on the parcels which caused disconnected parcels.
I will appreciate if you help me to solve this problem.
kind regards,
Najme
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Message: 2
Date: Thu, 17 Dec 2020 14:27:36 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] need assistance to decode QDEC results
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <e914c43c-e317-147d-41cc-faf9b0133606@mgh.harvard.edu>
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It depends on the order that you specified them. You will have four groups
SczUrban
SczRural
HVUrban
HVRural
The interaction will be of the form
(SczUrban-SczRural)-(HVUrban-HVRural)
Look in the y.fsgd to see what the order of the classes is. You can then look in the contrast folder at C.dat to get the + and - 1s used in the contrast.
On 12/9/2020 12:58 PM, vittal korann wrote:
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Dear FreeSurfer experts,
I was running group interaction (for diagnosis and birthplace) in QDEC with gyrification as a dependent variable and age, gender as nuisance factors.
In diagnosis, we have 2 groups: i) schizophrenic patients ii) healthy volunteers.
Similarly, birthplace has 2 groups: i) urban ii) rural birth
For the above-said design, I got reddish yellow color results in the display tab of Qdec.
So, my query is that do results indicate that patients who were born in urban have a higher gyrification index than healthy volunteers who born in urban or something else? Do I sound correct in decoding the interaction results? If not please let me know the exact meaning of the results.
Looking forward to hearing from you.
Thanks,
Vittal
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Message: 3
Date: Thu, 17 Dec 2020 14:31:03 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Cortical thickness volume ROI to surface
{Disarmed}
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <0b70fc8e-b0ef-b16c-ba84-c1f6aaabbf7a@mgh.harvard.edu>
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fslregister should have printed out a tkregisterfv command to use to check the registration. Does that registartion look ok or not? If not, try mri_coreg instead of fslregister
On 12/11/2020 6:11 AM, Alina Rojas wrote:
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Hello Douglas,
Thank you for your response. I seem to be having problems with registration. I tried:
#flirt -in T1w.nii.gz -ref fsl/data/standard/MNI152_T1_2mm -out T1w_MNI.nii.gz -omat T1w_MNI.mat#fnirt --in=T1w.nii.gz --aff=T1w_MNI.mat --cout=nonlinear_transf --config=T1_2_MNI152_2mm#applywarp --ref=/fsl/data/standard/MNI152_T1_2mm --in=T1w.nii.gz --warp=nonlinear_transf --out=warped_strucctural
->>this looks good, the ROI is where I expect it to be.
[cid:part1.A0715EA3.F1997B19@mgh.harvard.edu][cid:part2.832C2D59.D5A0FCB1@mgh.harvard.edu]
#fslregister --s fsaverage --mov T1w_MNI.nii.gz --reg /work/bav5809/subjects/severe/freesurfer_output/hand/${SUBJECTID}-${SESSIONID}/tmp.dat
#tkmeditfv fsaverage T1.mgz \
-overlay M1_L_bin.nii.gz \
-overlay-reg tmp.dat \
-fthresh 0.5 \
->>the problems seems to be in the registration because that does not look good.
[cid:part3.9F6D9A90.70B6235B@mgh.harvard.edu]
Can you help me find the problem?
Many thanks,
Alina Rojas
Am 29.11.2020 um 18:17 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>:
Have you checked that the output of each of the stages is correct? Eg, does mydata_T1.nii.mgz overlay with MNI152 and with ROI_MNI? At the end of fslregister, there will be a tkregister command to visualize the regsitration. Do those look ok?
On 11/17/2020 4:48 AM, Alina Rojas wrote:
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Thank you for your response! Here the commands:
#register image to MNIspace
flirt -in mydata_T1.nii.gz -ref fsl/data/standard/MNI152_T1_1mm -out mydata_T1_MNI.nii.gz -omat mydata_T1_MNI.mat
#Create a registration from the ROI-anatomical volume to a freesurfer template subject
fslregister --s fsaverage --mov mydata_T1_MNI.nii.gz --reg tmp.dat
#Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI surface overlay.
mri_vol2surf --mov ROI_MNI.nii.gz --reg tmp.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.ROI_MNI.mgh ?noreshape
tkmeditfv fsaverage lh inflated -overlay lh.fsaverage.M1_L.mgh -fthresh 0.5
I tried with another threshold, and to change it while in Freeview and it?s either the whole surface with the overlay or none.
Thank you for your help!
Alina Rojas
Am 16.11.2020 um 17:04 schrieb Douglas N. Greve <dgreve@mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>>:
please send the command line
On 11/16/2020 7:20 AM, Alina Rojas wrote:
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Hello Freesurfer experts,
I am attempting to register a ROI (.nii) to the surface of fsaverage to get the statistical output on the cortical thickness. I followed your instructions on MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness<https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5utz9wmCB_PLEjDtsOmyziziVBQRSmBgczrdyk56eX0vaBWBNP1iIevBdxOho3o-JJ64DuVK1J6XpzIFNVqqzBDHDrU6O2cYjWTNnglb4Ow4OIdXr5Qq28eboicyUSvLl2KmB0P0lQY9abQIfjX6hs_1Q1FvwX1Tx7YnGwsbJIgqcpDRG0dkvqZc0pgeiBQbnNjLadwozbHME2Ale8Kt0-V-I2Urmgq5zbEhzlAPvCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness> but after mri_vol2surf I get this message, I can?t visualize the ROI on the surface. I I?m using Freesurfer 7.0.1. How can I solve this? Thank you, Alina Rojas.
srcvol = M1_L.nii.gz
srcreg = tmp.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = 0.5
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
INFO: using NIfTI-1 qform
Done loading volume
INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0.
Input reg is register.dat
-------- original matrix -----------
1.00000 0.00000 0.00000 2.49380;
0.00000 0.00000 1.00000 -22.50500;
0.00000 -1.00000 0.00000 -9.53872;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Reading surface /fsaverage/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
1 0 0 1
using old
2 0.1 0 1
using old
3 0.2 0 1
using old
4 0.3 0 1
using old
5 0.4 0 1
using old
6 0.5 0 1
using old
7 0.6 0 1
using old
8 0.7 0 1
using old
9 0.8 0 1
using old
10 0.9 0 1
using old
Done mapping volume to surface
Number of source voxels hit = 75073
Writing to lh.fsaverage.M1_L.mgh
Dim: 163842 1 1
surfcolor: Subscript out of range.
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Message: 4
Date: Thu, 17 Dec 2020 14:34:29 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in selxavg3-sess
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <7226e63d-3bff-bbd2-a211-6d9561a6b6fc@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Are there presentations that are simultaneous?
On 12/12/2020 3:19 AM, Nina Khatibi wrote:
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Hi,
I'm using a functional analyse with selxavg3-sess, i have 25 subjects and each subject contains 15 runs, I've done plenty of analyses with different paradigm files, but now with a paradigm file of 5 conditions, I face an error on subject 22 run 12, which I can not solve.I wonder if you can help me.
I'm using macbook pro 2018, macOS Mojave 10.14.6 and freesurfer-darwin-macOS-7.1.1-20200811-8b40551
outanadir = /Volumes/ADATA/FunctionalData/Subject22/bold/fsaverage5Con2Sec.lh/pr012
Excluding 4 points
ERROR: fast_st2fir: two or more presentations are simultaneous
ERROR: creating FIR design matrix for Condition01
Dot indexing is not supported for variables of this type.
Error in flac_customize (line 354)
if(~isempty(flacnew.TFmtx))
Error in fast_selxavg3b (line 179)
flac = flac_customize(flac);
>> ------------------------------------------
ERROR: fast_selxavg3() failed\n
Regards,
Nina
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------------------------------
Message: 5
Date: Thu, 17 Dec 2020 14:36:39 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] cannot find
freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <fb0d461f-dc8c-9ce7-e906-8917950e25e4@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
The GPU stuff may or may not work. It was hard to maintain because the GPUs kept changing so much, and it would not surprise me that the code from 5.3 is incompatable with GPUs today. But it looks like the error is that it could not find a file. Does that file actually exist?
On 12/12/2020 3:04 PM, Caspar M. Schwiedrzik wrote:
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Hi!
I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am getting a strange error that I would love to get your input on: cannot find freesurfer/average/RB_all_2008-03-26.gca
Neither the file nor the path exist.
This is the entire input and output:
recon-all -s hum_14600_parallel -i /neuro_tools/freesurfer/subjects/hum_14600/mri/011/mp2rage.nii -all -use-gpu
Testing for CUDA device:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_Sep_21_17:28:58_PDT_2012
Cuda compilation tools, release 5.0, V0.2.1221
Driver : 10.0
Runtime : 5.0
Acquiring CUDA device
Using default device
CUDA device: Tesla K40m
======= NUMBER OF OPENMP THREADS = 1 =======
stable5
NVIDIA driver version info:
NVRM version: NVIDIA UNIX x86_64 Kernel Module 410.79 Thu Nov 15 10:41:04 CST 2018
ERROR: cannot find /neuro_tools/freesurfer/average/RB_all_2008-03-26.gca
Is there some documentation on how to set up the environment beyond LD_LIBRARY_PATH? Could that be the issue? Everything works fine without the -use-gpu flag.
Thank you! Caspar
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Message: 6
Date: Thu, 17 Dec 2020 15:38:46 +0100
From: "Caspar M. Schwiedrzik" <cschwiedrz@rockefeller.edu>
Subject: Re: [Freesurfer] cannot find
freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3
{Disarmed}
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+bX-39LXRwm97VponUybd+L-jUAKUNvM8voQfvQxrxLSi8o8g@mail.gmail.com>
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Hi Doug,
it turns out part of the v5.3 installation had been accidentally deleted.
After restoring the file, it works fine, and I am happy to report the the
GPU versions work (with CUDA 5).
Thanks!
Caspar
Am Do., 17. Dez. 2020 um 15:37 Uhr schrieb Greve, Douglas N.,Ph.D. <
DGREVE@mgh.harvard.edu>:
> The GPU stuff may or may not work. It was hard to maintain because the
> GPUs kept changing so much, and it would not surprise me that the code from
> 5.3 is incompatable with GPUs today. But it looks like the error is that it
> could not find a file. Does that file actually exist?
>
> On 12/12/2020 3:04 PM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi!
> I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am
> getting a strange error that I would love to get your input on: cannot
> find freesurfer/average/RB_all_2008-03-26.gca
> Neither the file nor the path exist.
>
> This is the entire input and output:
>
> recon-all -s hum_14600_parallel -i
> /neuro_tools/freesurfer/subjects/hum_14600/mri/011/mp2rage.nii -all -use-gpu
> Testing for CUDA device:
> nvcc: NVIDIA (R) Cuda compiler driver
> Copyright (c) 2005-2012 NVIDIA Corporation
> Built on Fri_Sep_21_17:28:58_PDT_2012
> Cuda compilation tools, release 5.0, V0.2.1221
>
> Driver : 10.0
> Runtime : 5.0
>
> Acquiring CUDA device
> Using default device
> CUDA device: Tesla K40m
>
>
> ======= NUMBER OF OPENMP THREADS = 1 =======
> stable5
>
> NVIDIA driver version info:
> NVRM version: NVIDIA UNIX x86_64 Kernel Module 410.79 Thu Nov 15
> 10:41:04 CST 2018
>
> ERROR: cannot find /neuro_tools/freesurfer/average/RB_all_2008-03-26.gca
>
> Is there some documentation on how to set up the environment beyond
> LD_LIBRARY_PATH? Could that be the issue? Everything works fine without the
> -use-gpu flag.
>
> Thank you! Caspar
>
>
> _______________________________________________
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Message: 7
Date: Thu, 17 Dec 2020 14:40:57 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] group analyses {Disarmed}
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <8ede4058-1020-1a32-398a-0e44a37a1e47@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
If you want to apply etiv correction when extracting the cortical volume with mris_preproc, just add --etiv to the command
On 12/14/2020 9:59 AM, Sara Lyn wrote:
External Email - Use Caution
Hi
Thank you for your response. How do I correct this extracted volume for intracranial volume (etiv)?
Thank you
Sara
On Sun, Dec 13, 2020 at 12:30 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> wrote:
When you run the thickness analysis with multiple comparisons correction (mri_glmfit-sim), it will create "ocn" files. These will be clusters of the significant areas. You can use this to extract other information. If you want volume, then run mris_preproc using the --meas volume flag, the apply the ocn to this file using mri_segstats using the --avgwf and --accumulate flags (and --exclude 0). This will give you a nsubjects-by-nclusters text file where each entry is the volume for that subject/cluster
On 12/8/2020 10:48 AM, Sara Lyn wrote:
External Email - Use Caution
Hi Joceyln,
I'm not trying to run a new group analysis but want to extract volume values from significant thickness ROIs obtained from a thickness group analysis.
Thank you
Sara
On Tue, Dec 8, 2020 at 10:38 AM Mora, Jocelyn S. <JSMORA@mgh.harvard.edu<mailto:JSMORA@mgh.harvard.edu>> wrote:
Hi Sara,
You may want to try --meas volume in place of --meas thickness when running mris_preproc.
I would also recommend looking at our ROI Analysis<https://secure-web.cisco.com/1g2kRJfau7HjSgmWu9k1y2XTwIMcBGIA-XwH0H7VI8zAxTQzb4aOSMDp6R8Jfi0Po3NMRSG9C0LtNtm6-woQEgwl-cwbWL8_TXyPMqoIvev2Gk5xKmwgW8IuFaQjw69Y3FCuRKwDVHOMSTjPP3MAi29ARxwq_LRpLO7bxtHZW1jAyuRNtrmD4erpddTzuHg3F62ADZRqOYBLyWHlzBBPqp7yCdVoH4o7Gia01u1hT-aoNc8JHUlKMud7cMQz4MsOZAOv64wbXgkh8bAUP0bhvAg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROIV6.0> tutorial and Volumetric Group Analysis<https://secure-web.cisco.com/1tHYiEwJMSx00y8RdQYJIg0nUV5bkFIzrk567zMxayemPQ09G48rqDnWqw4E6yrlMBJLktsyeyMdqA8GdbPJDzXQF7xx_UyMd7vKwH4Re9TF4tJdv1FaNzemfK7i5QI7Psfkt891h5PytK7i7KSod464UAFFriIC4NrIYk_lzZGh6ljc-y-Q3jIxXf0RbP6lDllgUJaJ3XS9i_BCSUoZAUhpAyzrfLoi1XWxtXjxQl_iCBoocEJOpE_SFyFHLaZYUyWgGShrqcIZTYr-w7rqWSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FVolumetricGroupAnalysis%3Fhighlight%3D%2528thickness%2529%257C%2528volume%2529%257C%2528measure%2529> tutorial. Please let us know if you are
still having trouble.
Cheers,
Jocelyn
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Sara Lyn <saralyn543@gmail.com<mailto:saralyn543@gmail.com>>
Sent: Monday, December 7, 2020 10:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] group analyses
External Email - Use Caution
Hi FS developers,
I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte carlo) for a surface based thickness group analysis. I am trying to extract volume measures from the same significant thickness ROIs. Is there any way to do this? Thank you!
Sara
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End of Freesurfer Digest, Vol 202, Issue 30
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