[Freesurfer] FSGD file and constrast

[Steve Petersen]

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Dear FreeSurfer experts,

I have MRI data of one group of subjects and would like to evaluate
positive and negative correlations between cortical thickness and some
biomarkers by excluding the potential effects of age and sex. I followed
the FS tutorials (
https://secure-web.cisco.com/1Y5TdIEJ9ARZSn2I1-6PLi22V0MhAKTkmre4K1MKlAmgQhOuo0ABTOlLkmv8yUG5GmoiUoT9vLUZqBd9teEjxGtg_njtrd6B0mEYG13180vZxMNydCJu2Azma_EkZPMxwc5CFJBltb1lnb8L5vkrl-R1voR9oApszFzwU_zwh_pXekEYhB26v1kEEcskCUXReKdVI2fKKTYtXLeVqHMamKR_6MyIoviEX04nL1i5qnT2gOQy3fI--HiEk3tt2PEWA3Y8G7UYYgbB_AGz6eFV_4-NCzry-9HKiGgOFZj8ThtCIKt_RBdnTcClL2u9cVgXeCV11MxINzrulyu_JmXrqoQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisDemographics%23DODSDesignMatrix)
and have read previous posts on the FS´s mail archive but I would
appreciate if you can check if my FSGD file and contrasts are right.


The FSGD file looks as follows:

GroupDescriptorFile 1
Title CTh_Bioma
Class Female
Class Male
Variables age biomarker
Input 4009 Female 60 222.0
Input 4014 Male 70 195.6
Input 4022 Male 68 230.2
Input 4027 Female 65 250.0
Input 4039 Male 62 205.6
Input 4001 Male 63 270.2
Input 4002 Male 78 245.5
Input 4004 Male 66 234.1
Input 4050 Female 62 210.0


And these would be my contrasts:

positive correlation between thickness and the biomarker: 0 0 0 1
negative correlation between thickness and the biomarker: 0 0 0 -1



Thank you very much in advance.


Best regards,

Steve.
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[Freesurfer] Autorecon-pial with T1w and T2w images

[Steve Petersen]

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Dear FreeSurfer experts,

After reviewing and manually editing the recon-all outputs in freeview, I'm
going to re-run the recon-all command with the autorecon-pial flag. My
question is, does the autorecon-pial also take into account the T2w image
or does it only consider the T1w image?. In case of not considering both
images (T1w and T2w), is there a way to run the autorecon-pial with both
images in order to get a more accurate pial surface segmentation?

Thank you very much in advance.


Best regards,
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[Freesurfer] Recon-all in post stroke aphasic patients.

[Steve Petersen]

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Dear FreeSurfer experts,

I would like to run the recon-all command in MRI images of post-stroke
aphasic patients. Should I use a particular flag in the recon-all command
to avoid important errors during cortical reconstruction?. We are only
interested in the right hemisphere (where there is no brain injury), can I
conduct the recon-all only in the right hemisphere?.

Any help would be appreciated.

Thank you very much in advance.

Best regards,

Steve.
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[Freesurfer] T1w/T2w ratio maps: acquisition parameters T1w and T2w

[Steve Petersen]

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Dear FreeSurfer experts,

I would like to calculate myelin maps using the ratio between T1w and T2w
scans. However, the acquisition parameters of the T2w images are slightly
different (e.g.* voxel size T1w* = 1mm3* vs* *voxel size T2w* = 0.35 mm3 ;*
T1w matrix:* 240 x 240 *vs* *T2w matrix:* 640 x 640). The first step of the
protocol would involve a robust registration between the two MRI images
(e.g. bbregister method) which would lead to a downsampling of the T2w
images. My question is, could I conduct a reliable analysis of T1w/T2w
ratio maps despite these differences in the acquisition parameters between
both MRI sequences?.

Thank you very much in advance.

Best regards,

Steve.
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Re: [Freesurfer] Cohen´s D effect size

[Steve Petersen]

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Dear Freesurfer experts,

I would really appreciate it if anyone can give me some guidance about this
question that I posted a few days ago. I conducted a One-way ANOVA and now
I would to report the Cohen's D effect size for each pairwise comparison
(t-tests). For that purpose, I estimated the Cohen's D effect size of
significant clusters using the suggested command
<https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html>:


fscalc gamma.mgh div rstd.mgh -o cohensd.mgh

Now, I get the cohensd.mgh file but I am not able to open this file. How
can I see the particular effect size of each significant cluster included
in the sig.cluster.summary file?.

Thank you very much in advance for your time!

Best regards,

Steve,

El mié, 15 dic 2021 a las 19:14, Steve Petersen ()
escribió:

> Dear Freesurfer experts,
>
> I am attempting to estimate the Cohen's D effect size of significant
> clusters using the suggested command
> <https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html>:
>
>
> fscalc gamma.mgh div rstd.mgh -o cohensd.mgh
>
> Now, I get the cohensd.mgh file but I am not able to open this file. How
> can I see the particular effect size of each significant cluster included
> in the sig.cluster.summary file?.
>
> Thank you very much for your help!
>
> Best regards,
>
>
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[Freesurfer] Cohen´s D effect size

[Steve Petersen]

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Dear Freesurfer experts,

I am attempting to estimate the Cohen's D effect size of significant
clusters using the suggested command
:


fscalc gamma.mgh div rstd.mgh -o cohensd.mgh

Now, I get the cohensd.mgh file but I am not able to open this file. How
can I see the particular effect size of each significant cluster included
in the sig.cluster.summary file?.

Thank you very much for your help!

Best regards,
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[Freesurfer] Freesurfer: Re-run recon-all in older versions

[Steve Petersen]

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Dear all,

We conducted the recon-all and applied a quality control protocol in
several subjects using the FSurfer 6 version. Now, we would like to run the
recon-all again on an older version of FSurfer (5.3 v) but considering the
edits we made on those previous recon-all. Is this possible?, and if so,
what would be the command?

Thank you very much in advance.

Best regards,

Steve.
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[Freesurfer] C.Thickness: Statistical analyses with three groups

[Steve Petersen]

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Dear Freesurfer experts,

My goal is to compare the cortical thickness between three groups. For that
purpose, I performed whole brain analysis with a F-contrast to evaluate a
group effect. Since the F-test was significant, I performed pairwise
comparisons to evaluate the direction of these differences. However, I
noticed that some brain areas that are significant in one pairwise
comparison (that are consistent with our hypothesis) were not significant
in the F-test. I am a bit lost about how to proceed in this situation, can
I report significant results in the pairwise comparison that were not
previously significant in the F-contrast or do I need to perform the
pairwise comparisons by applying a mask to the brain areas where there were
significant results in the F-test?

Apologies for asking this simple question, I am a beginner in statistical
analysis with MRI data.

Thank you very much for your help.

Best regards,
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[Freesurfer] SAMSEG for Alzheimer´s Disease study

[Steve Petersen]

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Dear Freesurfer experts,

We are working with a large MRI dataset (FLAIR, T1) of healthy adults and
adults with mild cognitive impairment. Can we use SAMSEG to segment white
matter lesions in this population?.


Thanks for your help!

Best,

Steve.
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[Freesurfer] Correlation between thickness and csf_measures: vector

[Steve Petersen]

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Dear Freesurfer experts,

I am conducting a cortical thickness study in three groups. After
performing the between-group analyses, I would like to evaluate the
possible correlation between cortical thickness and the levels of some csf
measures. To do this I included one column in the FSGD file

GroupDescriptorFile 1
Title OSGM
Class N
Class AD_PREC
Class AD_PLUS
Variables CSF_A_measure
Input 4048 N 1730.00
Input 4102 N 2217.00
Input 4122 PREC 652.00
Input 4146 PREC 695.00
Input 4198 PREC 938.00
Input 5049 AD_PLUS 909.00
Input 5080 AD_PLUS 987.00
Input 5096 AD_PLUS 942.00
Input 5101 AD_PLUS 881.00
Input 5232 AD_PLUS 715.00
And so on


In order to test the possible positive relation between the CSF_A_measure
and the cortical thickness, that is, *does the correlation between
thickness and csf_A_measure differ from zero?, *I would use the following
vector and commands for the left hemisphere.



*Question 1.* Please, can you verify if this vector and commands are
correct.

correlation_vector.mtx -> 0 0 0 1 1 1

mris_preproc --fsgd J3.fsgd \
  --cache-in thickness.fwhm10.fsaverage \
  --target fsaverage \
  --hemi lh \
  --out lh_J3G_thickness.10.mgh \

mri_glmfit \
--y lh_J3G_thickness.10.mgh \
--fsgd J3.fsgd \
--C correlation_vector.mtx \
--surf fsaverage lh \
--cortex \
--glmdir 01_lh_thickness_results\

mri_glmfit-sim \
  --glmdir 01_lh_thickness_results \
  --sim mc-z 1 2.3 mc-z.pos \
  --sim-sign pos --cwpvalthresh 0.05\
  --2spaces --overwrite \


*Question 2:* I tried to run these commands with the permutation method but
the terminal gave to me a warning message saying that the matrix is not
orthogonal and if I really want to run the analysis I should add the
--perm-force argument, in this case should I use other method or can I use
the --perm-force safetely?.


Thank you very much for your help in advance.


Best regards,



Steve,
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[Freesurfer] Hippocampal subfields questions

[Steve Petersen]

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Dear Eugenio,

Just two simple questions about hippocampal subfields:

Q1. The volume of each hippocampal subfield is exported in mm3?

Q2. I would like to compare hippocampal subfields volume measures between
three groups by including the eTIV as covariate. Can I perform this group
analysis by using the command line (with mri_glmfit command as for the
thickness for example)?. In that case should I include some specific
argument to consider in the analysis the hippocampal subfield stats of each
subject?.


Thank you in advance.


Best,

Steve
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[Freesurfer] Group Analysis: Comparing four groups

[Steve Petersen]

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Dear Freesurfer experts,

This is the first time I perform group analysis in Freesurfer. My aim is to
compare the cortical thickness in four groups matched in age, sex and years
of education using the Monte Carlo multiple comparisons correction. I tried
to follow the Freesufer tutorials
 to
perform this group analysis and I would be really grateful whether someone
can verify that all steps are correct. For example, for the cortical
thickness (smooth = 15 FWHM) of the left hemisphere, the four steps that I
followed were:

STEP 1. Assemble the cached Data (mris_preproc) using the fsgd file

mris_preproc --fsgd STUDY_4groups.fsgd \
  --cache-in thickness.fwhm15.fsaverage \
  --target fsaverage \
  --hemi lh \
  --out lh_J4G_thickness.15.mgh \

STEP 2. Perform a GLM Analysis (mri_glmfit)

mri_glmfit \
--y lh_J4G_thickness.15.mgh \
--fsgd STUDY_4groups.fsgd \
--C *group.effect.mtx* \
--surf fsaverage lh \
--cortex \
--glmdir left_hemisphere_thickness_results\


STEP 3. Perform Monte Carlo simulation

mri_glmfit-sim \
  --glmdir left_hemisphere_thickness_results \
  --sim mc-z 1 4 mc-z.abs \
  --sim-sign abs --cwpvalthresh 0.05\
  --overwrite \


*QUESTIONS:*

1. Have I followed the steps to perform the analysis correctly or do you
think I forgot some important flag?


2. Before test differences between two groups (eg. group1 > group 2 with
the vector 1 -1 0 0) I would like to test any group effect. For that
purpose, I created the group.effect.mtx contrast file (see below), is
correct?

1 -1 0 0
0 1 -1 0
0 0 1 -1


Any help would be appreciated.

Best regards,


Steve
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[Freesurfer] Results summary in QDEC

[Steve Petersen]

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Dear Freesurfer experts,

I performed group analysis in QDEC in order to compare cortical thickness
between two groups using the Monte Carlo Z simulation correction. My
question is, where is located the z-score of each significant cluster?
Maybe in the second column named as Max?. Below you can find an example. In
this case z-scores of the precuneus and the inferior parietal would be
3.422 and 3.926 respectively?


Input
 
/usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-HC-ad_plus-Intercept-thickness/sig.mgh
# Frame Number  0
# srcsubj fsaverage
# hemi lh
# surface white
# group_avg_surface_area 82220
# group_avg_vtxarea_loaded 1
# annot aparc
# SUBJECTS_DIR /usr/local/freesurfer/subjects
# SearchSpace_mm2 75146
# SearchSpace_vtx 146493
# Bonferroni 0
# Minimum Threshold 2.3
# Maximum Threshold infinity
# Threshold Signabs
# AdjustThreshWhenOneTail 1
# CW PValue Threshold: 0.05
# Area Threshold0 mm^2
# CSD thresh  2.30
# CSD nreps1
# CSD simtype  null-z
# CSD contrast NA
# CSD confint  90.00
# Overall max 4.16102 at vertex 61133
# Overall min -1.24867 at vertex 155746
# NClusters  2
# FixMNI = 1
#
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWPCWPLow
   CWPHi   NVtxsWghtVtx   Annot
   13.422   78695820.44-11.2  -54.8   49.4  0.00250
 0.00190  0.00310   1664 4553.35  precuneus
   23.926   52042733.99-30.8  -66.6   40.7  0.00410
 0.00330  0.00490   1190 3620.13  inferiorparietal

Simulation complete.



Thanks in advance.

Best regards,


Steve.
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Re: [Freesurfer] Correlation between Hippocampal subfields - behavioural test

[Steve Petersen]

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 Dear Eugenio,

Thank you for your quick response. Sorry but I am not completely sure if I
understood correctly your response. What do you mean with "demeaning" the
eTIV first?.

If I understood, a good choice would be to correct the subic_volume before
perform the regression using the folliwng formula:

subic_vol = average_eTIV_allsample * subic_vol / eTIV_subject


Thank you.

Best,


Steve.




El mié., 22 abr. 2020 a las 17:35, Steve Petersen ()
escribió:

> Dear Freesurfer experts,
>
> I would like to perform a correlation between the volume of subiculum and
> some behavioural measures. Before making that correlation, is it necessary
> to correct the subiculum volume with the eTIV? I have thought of doing it
> by scaling the subiculum volume as follows:
>
>
>   *subic_vol = mean_eTIV_group * subic_vol / eTIV_subject *Is
> correct??
>
> mean_eTIV_group = eTIV average of the group to which the subject belongs.
>
> Thanks in advance.
>
> Best regards,
>
> Steve.
>
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[Freesurfer] Correlation between Hippocampal subfields - behavioural test

[Steve Petersen]

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Dear Freesurfer experts,

I would like to perform a correlation between the volume of subiculum and
some behavioural measures. Before making that correlation, is it necessary
to correct the subiculum volume with the eTIV? I have thought of doing it
by scaling the subiculum volume as follows:


  *subic_vol = mean_eTIV_group * subic_vol / eTIV_subject *Is correct??

mean_eTIV_group = eTIV average of the group to which the subject belongs.

Thanks in advance.

Best regards,

Steve.
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[Freesurfer] Volume correction with Intracranial volume

[Steve Petersen]

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Dear Freesurfer experts,

I would like to perform external analysis with the hippocampus,
parahipocampus and entorhinal volume. As I understand its the hipocampo
volume should be corrected using the subject´s intracranial volume.


1. How do you recommend correcting the volumes (hippocampus, parahipocampus
and entorhinal cortex) with the intracranial volume? Maybe correcting the
volume by scaling with the EstimatedTotalIntraCranialVol?

2. Is necessary to correct the cortical thickness measurements with the
intracranial volume?

Thanks for your help.


Best regards,
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Re: [Freesurfer] Hippocampal subfields: exporting results

[Steve Petersen]

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Dear Eugenio,

I noticed what was the problem. I used freesurfer dev version with the
following command:

segmentHA_T2.sh

I tried to export the hippocampal and amygdala results of several subjects
with these commands and now everything works fine.

quantifyHAsubregions.sh hippoSf HIPO-AMY hippocampal_results.txt

quantifyHAsubregions.sh amygNuc HIPO-AMY amygdala_results.txt


Is there some difference between the *segmentHA_T2.sh*  that I used and the
command of the website? In that case I would like to use the most
appropriated.


recon-all -s  *-hippocampal-subfields-T2*  

 Thanks in advance.


Best regards,
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[Freesurfer] Hippocampal subfields: exporting results

[Steve Petersen]

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Dear Freesurfer experts,

I used the freesurfer dev version to estimate hippocampal subfields using
mode B (additional scan).

All have worked fine although when I tried to export the results I can not
find the txt file created

This is the output


rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh HIPOAMYG
HipoAmyg_results.txt /Applications/freesurfer/subjects/4001T1

Gathering results from subjects in:

   /Applications/freesurfer/subjects/4001T1

Using the suffix name:

   HIPOAMYG

And writing them to:

   HipoAmyg_results.txt




Where is saved the HipoAmyg_results.txt file?? I have searched it and I
can't find it...


Excuse me for this basic question.



Thanks in advance.



Best regards,
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[Freesurfer] T2 in recon-all: command to correct pial surfaces errors

[Steve Petersen]

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Dear Freesurfer experts,

I used t2 image as input in subjects that have already been processed
without them following the instructions of the website. Although pial
surface segmentation has improved there is still some error. After edit the
brainmask.mgz file in Freeview (recon edit option), what command should I
use  to correct the pial surfaces obtained after the -T2pial flag?

I tried to use the -autorecon-pial command to correct the edits but I think
that this command only takes into account the T1, is that right?


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[Freesurfer] Freesurfer dev version: Hyppocampus, amygdala and thalamus segementation

[Steve Petersen]

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 Dear Freesurfer devs,

We are considering segmenting with the Freesurfer 6 dev version the
hippocampus, the amygdala and the thalamus of several subjects who have
already done the recon-all. Since we have a T1 image and T2 image with
smaller voxel size, we have thought about using the *mode B: segmetation
with an additional scan* as explained in the freesurfer webpage. In
addition to voxel size, both images have slight differences in acquisition
parameters. Taking into account this situation we have these questions:

- Since there are other slightly different parameters between image T1 and
T2 in addition to voxel size (e.g. matrix size), it is correct to use B
mode with additional scan or we should use multispectral segmentation?

- Is it necessary to make some previous modification on some image before
running the script segment_HA.sh (e.g. coregister both images)?

- Is there a quality control that you can recommend after segmenting these
structures?


Thanks for your help!


Best regards,
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[Freesurfer] Local Gyrification Index: freesurfer version

[Steve Petersen]

External Email - Use Caution

Dear Freesurfer experts,

What freesurfer version do you recommend to perform the local gyrification
index, version 6 or 6 development version?


Thanks in advance.

Best regards,
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[Freesurfer] Freesurfer V6 installation: ubuntu virtual machine

[Steve Petersen]

External Email - Use Caution

Dear Freesurfer experts,


Just a simple question, is possible to install the Freesurfer (Version 6)
in a virtual machine of ubuntu?

Thanks in advance,


Best regards,

Steve
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