[Freesurfer] Changing colour of clusters generated after MonteCarlo Correction

[Arsenije Subotic]

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Dear experts,


Is it possible to change the colour of the clusters generated after using Monte 
Carlo Corrections? I would like to have it either blue or red to represent 
thinning or thickening respectively, since there are many different cluster 
colours that may confuse readers at first glance.


Thank you,

Arsenije



---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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Re: [Freesurfer] Longitudinal Two Stage Model Question

[Arsenije Subotic]

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Sorry,


I was actually able to compile a FSGD file that has a single line for each 
subject (containing the fsid base) along with gender and age at baseline. I ran 
this through the mris_preproc command 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) in order 
to stack the spc files which were previously cached.


I guess my question really is can I now simply continue on and use the 
mri_glmfit instructions on the group analysis tutorial page or is there a 
special procedure because I am dealing with longitudinal data? I was planning 
on simply using contrasts i had designed before for my cross-sectional 
analysis, controlling for age at baseline and gender.


Thanks and my apologies for all the questions!

Arsenije


---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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[Freesurfer] Longitudinal Two Stage Model Question

[Arsenije Subotic]

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Hello,


I am doing a longitudinal analysis for which I have already qcached my data 
using the long_mris_slopes command.


I am having issues figuring out how to run the mri_glmfit command for my 
longitudinal two stage model. I'm interested in comparing the spc over time 
between two groups after controlling for age and gender. The tutorial on the 
longitudinal two stage model however only shows how to do it for one sample.


Am I still expected to use contrasts and make glm directories like the 
cross-sectional group analysis tutorial suggests? I was just confused because 
the code is different. I have a longitudinal table so I assumed that would be 
enough, but do I still need to make a FSGD file that is basically the same as 
the longitudinal file?


Thank you for your help,

Arsenije



---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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[Freesurfer] One Group GLM Command Line Stream: correlating thickness with cognitive scores

[Arsenije Subotic]

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Dear experts,


I was hoping on examining the correlation between thickness and cognition 
within one group only and visualizing this using the command line stream. For 
my analysis I was planning on using cognitive scores that are adjusted 
according to published norms for age, sex, and education where possible. I do 
not want to use the scores as a covariate however, but simply find an 
association if possible. I'm assuming of course that I would use one of the one 
group FSGD formats

https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples?



Thanks!

Arsenije



---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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[Freesurfer] mri_glmfit-sim cluster correction threshold inquiry

[Arsenije Subotic]

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Hello,

I am planning on running a correction for multiple comparisons, and I was 
hoping to use a vertex wise cluster forming threshold of 1.3, however after 
reading more when I ran the mri_glmfit-sim —help command it recommends using 
the permutation test if you are planning on using 1.3 as a threshold. Is there 
any reason why it is not recommended to use the 1.3 cluster threshold? My study 
is fairly exploratory so I was hoping to be a bit more lenient when it comes to 
adjusting the threshold.

Thanks!
Arsenije

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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

[Arsenije Subotic]

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Hi Doug,

I realized this error a couple of days ago and now it works.

Thank you,
Arsenije


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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

[Arsenije Subotic]

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Hi,

I am still struggling to examine differences in thickness using the command 
line stream for my two groups after controlling for age and sex. I get the 
following error when running the command line:


ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd
CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh
--cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.00 (col 5), Max=611.699463 (col 4)
 The scale is much different between columns 5 and 4, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.
Column 5,  all values are 0
Column 6,  all values are 0
Columns 5 and 6 are the same




My design matrix is:
1 -1 0 0 0 0 (Examining difference in thickness after controlling for effects
of age and sex)

I’ve also attached the FSGD file that I’ve been using. Please let me know 
if there is something wrong with the file (although I have used a similar file 
without the covariates and did not have any issues).

Thanks!
Arsenije
---
Arsenije Subotic | MSc Student
Department of Clinical Neurosciences
Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada
Tel: (403) 918-6970
arsenije.subot...@ucalgary.ca<mailto:arsenije.subot...@ucalgary.ca>



CAA_CTRL_RH_Age_Sex.fsgd
Description: CAA_CTRL_RH_Age_Sex.fsgd
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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

[Arsenije Subotic]

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Hi Doug,


This is the bulk of the text I wrote initially in my first email:


Dear experts,

I have recently tried to use the command line to examine thickness differences 
between two groups after controlling for the effects of age and sex. I get the 
following error :

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd 
CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh 
--cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.00 (col 5), Max=611.699463 (col 4)
 The scale is much different between columns 5 and 4, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.
Column 5,  all values are 0
Column 6,  all values are 0
Columns 5 and 6 are the same

I did not get this error when I was only looking at the difference in thickness 
between the two groups, so I am guessing there is not an issue with the file 
format? Looking at the log, does this mean that I also need to demean the age 
variable? I was planning on running some contrasts looking at the interactions 
between group and age after controlling for sex etc. in order to see if I 
should go with a DOSS approach, but using those contrasts still gives me the 
same error.


Thanks,

Arsenije


---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

[Arsenije Subotic]

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Hi Doug,

Thank you for your reply.

My command was:
mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd CAA_CTRL_RH_Age_Sex.fsgd 
--C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh --cortex --glmdir 
CAA_CTRL_RH_Age_Sex_Unix.glmdir

My FSGD file is attached. It contains 2 classes and two covariates (Age and 
Sex).

My design matrix is:
1 -1 0 0 0 0 (Examining difference in thickness after controlling for effects 
of age and sex)
Please let me know what the issue is.

Best,
Arsenije


CAA_CTRL_RH_Age_Sex.fsgd
Description: CAA_CTRL_RH_Age_Sex.fsgd
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[Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

[Arsenije Subotic]

External Email - Use Caution

Dear experts,

I have recently tried to use the command line to examine thickness differences 
between two groups after controlling for the effects of age and sex. I get the 
following error :

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd 
CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh 
--cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.00 (col 5), Max=611.699463 (col 4)
 The scale is much different between columns 5 and 4, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.
Column 5,  all values are 0
Column 6,  all values are 0
Columns 5 and 6 are the same

I did not get this error when I was only looking at the difference in thickness 
between the two groups, so I am guessing there is not an issue with the file 
format? Looking at the log, does this mean that I also need to demean the age 
variable? I was planning on running some contrasts looking at the interactions 
between group and age after controlling for sex etc. in order to see if I 
should go with a DOSS approach, but using those contrasts still gives me the 
same error.

Thanks for your help!

Best,
Arsenije
---
Arsenije Subotic | MSc Student
Department of Clinical Neurosciences
Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada
Tel: (403) 918-6970
arsenije.subot...@ucalgary.ca<mailto:arsenije.subot...@ucalgary.ca>

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[Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

[Arsenije Subotic]

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Dear Freesurfer experts,


I am having issues choosing the spc option for my QDEC two stage longitudinal 
analysis as it is not there. The spc files are all present in my participants 
files and the Qdecrc file is in the qdec subdirectory containing the line 
long.thickness-spc. Is there a way to bypass this problem somehow?


Thank you,

Arsenije


---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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[Freesurfer] Calculating global thickness

[Arsenije Subotic]

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Dear experts,


When calculating global thickness, is it fine to simply use an average of 
lh.thickness and rh.thickness, or is it necessary to weight it according to the 
area of each hemisphere, so that the calculation is (lh.thickness x lh.area + 
rh.thickness x rh.area)/(lh.area +rh.area)?


Thanks!

Arsenije



---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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[Freesurfer] MRI sequence parameter difference and effect on cortical thickness values

[Arsenije Subotic]

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Dear experts,

For our study, we are planning on combining two different datasets to examine 
cortical thickness. There is a slight difference in the inversion time (400 vs 
650) and flip angle ( 8 vs 11) between the two datasets. I know that free 
surfer measurements are fairly consistent across different scanner types and 
strengths, but do you know if slight differences in mri sequence parameters 
have an affect on cortical thickness? I was planning on adding it as a 
covariate in our analysis just in case.

Thank you!
Arsenije

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[Freesurfer] Longitudinal processing: cannot find input volume error

[Arsenije Subotic]

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Dear Freesurfer experts,

I’m having problems with one of my participants when I am trying to create the 
base template for my longitudinal analysis. I get an error saying that the 
input volume (norm.mgz) for my followup time-point cannot be opened, even 
though the volume is not missing and loads perfectly fine in Freeview. Is this 
a bug or is something wrong with my norm.mgz volume by any chance? Please let 
me know.

Thank you,
Arsenije

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[Freesurfer] QDEC vs. Command Line Stream

[Arsenije Subotic]

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Dear experts,


I'm about to start my cortical thickness analysis for my groups, and I was just 
wondering what seems to be the consensus when it comes to using QDEC as opposed 
to using the command line stream? I've seen QDEC used plentifully in the 
literature, but I am also aware that it has less glm capability.


Thank you for any input!

Arsenije
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Re: [Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness

[Arsenije Subotic]

Hi Doug,

I am able to get up to the mrs_glmfit step of the Surface Based Group fMRI 
Analysis, but it does not indicate how a comparison should be made between the 
two groups that I have. It only gives information on how to perform a one 
sample group mean test (osgm). In addition, when you mention using a 
mrs_glmfit-sim command, does this also generate cerebrovascular reactivity 
values, or does it only provide cortical thickness values? I was also hoping 
that I could potentially visualize an average area of low BOLD CVR for both 
groups. Is that possible?

Thanks,
Arsenije
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[Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness

[Arsenije Subotic]

Dear experts,


I would like to create an average surface template of fMRI activation for two 
groups, and then determine areas of low cerebrovascular reactivity in my 
disease group, create a ROI, and extract the cortical thickness in this region 
and see how it compares to a control group by translating this ROI onto the 
control surface template. Do you have any tips or suggestions on how this 
workflow should be done?


I've currently been able to create an average surface for both groups, and I 
know how to create labels using tksurfer and to extract cortical thickness 
using mri_anatomical_stats. Is it possible however to create an ROI by only 
considering areas of low CVR/low activation in my disease group and calculating 
cortical thickness for this area, and then visualize it somehow and then 
translate this label onto the control group and doing the same?


I know it's a lot of questions, but going through the tutorial 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_tktools)
 it seems that I wasn't able to find exactly what I'm looking for.


Thank you for your help,

Arsenije

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[Freesurfer] Quality of fMRI registration

[Arsenije Subotic]

Dear experts,


When it comes to assessing the quality of fMRI integration in Freesurfer, is a 
value of > 0.5 considered a good registration? I was led to believe that from 
the multimodal tutorial website, and after checking the quality of my output I 
was satisfied with the result for each of my participants. However, I came back 
to the multimodal tutorial later after two weeks, and noticed that the page had 
been edited and now it says that any value <0.5 is considered a good 
registration. How would I go about resolving this issue, seeing as I visually 
inspected my output after each automatic registration and everything seemed 
fine? Most of my registration values were about 0.5-0.6.


Please let me know.


Thanks!

Arsenije
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[Freesurfer] Hippocampal subfields

[Arsenije Subotic]

Hi all

I would like to use subfield specific hippocampus maps that were produced Dr 
Iglesias's Lab: https://sites.google.com/site/jeiglesias/hippocampal-subfields

These maps are available via FreeSurfer, however our lab is trying to segment 
hippocampus subregions from already manually extracted hippocampuses. In other 
words, we have manually traced hippocampus masks in a NIFTI format that we 
would like to co-register with these maps.

How can I directly download subfield specific hippocampal atlases in a NIFTI 
format so that we can use non linear co registration after?

Thank you very much.

Look forward hearing from you,

Arsenije
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[Freesurfer] Potential ways to overlay perfusion ROIs onto cortical thickness maps

[Arsenije Subotic]

Dear experts,

I am trying to figure out the best way to overlay areas of low CVR reactivity 
and correlate that with cortical thickness measurements in those given regions. 
I was able to overlay our CVR map onto an inflated cortical surface in 3D and 
modify the configuration to see areas of low perfusion in blue. Using QDEC, I 
also know that you can manually trace an ROI and generate cortical thickness 
measurements within that ROI for a given subject. My question is, is it 
possible to manually trace an ROI in freeview? I tried doing it but it doesn't 
allow me to use the 'new ROI' when I use the drop down menu. And additionally, 
is there some way to accurately generate perfusion values within that ROI and 
then precisely transfer this ROI outline into QDEC so that the cortical 
thickness ROI is as close to the ROI in the CVR map as possible? Please let me 
know what you think.

Thanks!
Arsenije
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[Freesurfer] Control Points Not Working

[Arsenije Subotic]

Dear experts,

I’m currently performing quality control for my data, and most of my issues so 
far have been that in many cases adding control points has not been able to 
extend the white surface. I’ve also noticed that most of the regions where I 
have needed to add CPs are in the parietal regions of the brain. Does anyone 
know how many control points are usually recommended to be added? I have so far 
had cases where I have had to add hundreds of CPs and I have still had mixed 
success. 

Thank you,
Arsenije

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[Freesurfer] Qdec Table Loading Error

[Arsenije Subotic]

Dear experts,


I'm currently trying to import some of my data into Qdec in order to perform a 
group analysis on cortical thickness. All of my data was originally in an excel 
sheet and it had the following variables (fsid, gender, age, and thickness). I 
tried converting it into a file that would be opened with Qdec. I use a mac and 
I originally tried to export the file into text editor and I tried saving it as 
"qdec.table.dat", which had no problems being opened in text edit. However, 
when I tried loading it into qdec it gives me an error:"error loading the data 
table". I'm quite new to Qdec (this is my first week trying it). Is there some 
code that I can use to convert my file into a .dat file so that it can be 
compatible with qdec? I tried looking through the previous questions and trying 
some commands (for instance dos2unix -c mac qdec.table.dat, which supposedly 
replaces LF chars with CR chars).


Thanks for your help.


Arsenije
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[Freesurfer] Editing brainmask and white matter volumes when erasing dura

[Arsenije Subotic]

Dear experts,

After I erasing dura from my brain mask volume, I noticed that the white matter 
volume still had dura when I clicked on it. Is it usually fine to only edit the 
brain mask when we’re trying to erase the dura and regenerate the surfaces? The 
dura on the white matter volume has both the pial and white surfaces outlined 
and areas that have wm intensity of ~250. I know that the pial surfaces grow 
from the white matter so I figured that the -autorecon-pial command in the 
tutorial won’t solve my issue.

Thanks for your help.

Arsenije
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Re: [Freesurfer] Erroneous output after recon-all: Bad segmentation and surfaces

[Arsenije Subotic]

Hi Bruce and Emma,


I am running the latest version of Freesurfer, version 6.0. I will try manually 
erasing the voxels then and try re-processing the subject.


Thank you so much for your help.


Best,

Arsenije
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[Freesurfer] Skull-strip issues: commands not working

[Arsenije Subotic]

Dear experts,



I recently finished processing a subject for whom I had performed a skull-strip 
on the brainmask.mgz volume. I decreased the watershed parameter and re-examined
the brainmask and the portion of the skull was gone, although some dura was  
left over. I did a recon-all using the following command as the troubleshooting 
tutorial suggested to regenerate the surfaces based on the new brainmask.mgz 
volume:


recon-all  -autorecon-pial -subjid 



However, after the subject finished processing the surfaces were 
generated/outlined on the dura as well. I tried performing a g-cut command but 
it did not get rid of the dura. I also had issues with the subcortical 
segmentation as the ventricles were not completely segmented.


Thank you for your help.


Best,

Arsenije

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Re: [Freesurfer] Skullstrip commands not working {Disarmed}

[Arsenije Subotic]

Hi Bruce,


I performed the -autorecon-pial as a means of regenerating the surfaces as 
instructed on the Freesurfer skull strip tutorial. The brainmask.mgz file does 
not have the skull but it has some dura left over. The issue I had before was 
that the skull would re-appear after the subject finished processing and the 
surfaces would be outlined on the dura and skull.


Would it be okay if I could send screenshots of the my processed subject?


Thanks for your help.


Arsenije



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu 
Sent: Wednesday, November 22, 2017 11:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 165, Issue 35

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Today's Topics:

   1. Job opening: postdoc in AFNI group of NIH (P Taylor)
   2. Re: Problems when loading surface and mesh showingvertices
  (Rosalia Dacosta Aguayo)


--

Message: 1
Date: Wed, 22 Nov 2017 12:50:37 -0500
From: P  Taylor 
Subject: [Freesurfer] Job opening: postdoc in AFNI group of NIH
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hello-

The Scientific and Statistical Computing Core (a.k.a. the AFNI group) at
the NIMH, NIH (Bethesda, MD, USA) is lookin' to hire a postdoc,
particularly someone with C and/or C++ experience, with Python and OpenGL
skills also being quite useful.

If you like problem solving and working with a fun group of people, then
check out the attached advertisement for details.  (And please feel free to
forward on.)

--pt
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--

Message: 2
Date: Tue, 21 Nov 2017 18:25:17 +0100
From: Rosalia Dacosta Aguayo 
Subject: Re: [Freesurfer] Problems when loading surface and mesh
showing vertices
To: fis...@nmr.mgh.harvard.edu, Freesurfer support list

Message-ID:

[Freesurfer] Skullstrip commands not working

[Arsenije Subotic]

Dear experts,


I recently finished processing a subject for whom I had performed a skullstrip 
on the brainmask volume. I decreased the watershed parameter and re-examined 
the brainmask and the portion of the skull was gone, although some dura was 
left over. I did a recon-all using the following command:


recon-all  -autorecon-pial -subjid 


However, when recon was finished, I noticed that the skull re-appeared and the 
surfaces were outlined on it. I went back and tried g-cut to remove the little 
dura that was left over, but that also did not work. I tried varying the 
watershed parameters again but I keep getting the same result. Is there any 
other underlying issue that may be at fault?


Thanks for your help,

Arsenije
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[Freesurfer] XL Defect Correction

[Arsenije Subotic]

Dear Freesurfer experts,


During my recon-all I encountered a problem for one of my subjects, where the 
process got stalled at "CORRECTING DEFECT 12 (vertices=21293, convex hull=1791) 
XL defect detected...".


I've checked the output and it seems that skull-stripping hasn't been performed 
properly, but I do not know exactly if there are any other underlying issues. 
I've attached some screenshots for your consideration. I know that some defects 
can be fixed using manual correction or using control points, but I'm unsure 
exactly of what steps to take going forward.


I appreciate your help and any input.


Best regards,

Arsenije
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