[Freesurfer] visualizing a tract and a ROI

[Zeng, Qi]

External Email - Use Caution

Hi,

I was trying to demonstrate my findings by visualizing a significant tract
and a ROI at the same time on a single template or volume, for example,
left UNC and orbitofrontal overlaid on the T1-weighted.nii. However, I only
saw Freeview on tractography using -v and on surface using -f separately.
Is there a way to achieve this? If not, do you have any suggestions for
tools to use for visualizing a tract and ROI simultaneously? Additionally,
may I know which atlas is used for TRACULA and where I can download both
the 18 and 42 white matter tract atlases?


Thank you so much!
Best,
QZ
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[Freesurfer] outputs for recon-all of T1-weighted and intersubject registration

[Zeng, Qi]

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Hi Freesurfer experts,

If I just want to normalize, register, and segment the T1-weighted images
to the GM, WM, and CSF tissues, can certain steps be skipped from
recon-all, such as the inflation process? What is the output for the
segmentation of  GM, WM, and CSF tissues? is aseg.mgz or aparc+aseg.mgz
better? Following that, if I want to apply an affine transformation for all
subjects to a common template, is the following command line correct?

> mri_convert aparc+aseg.mgz aparc+aseg.nii.gz
> bet aparc+aseg.nii.gz my_structural.nii.gz
> flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in
my_structural.nii.gz -omat my_affine_transf.mat
> fnirt --in=aparc+aseg.nii.gz --aff=my_affine_transf.mat
--cout=my_nonlinear_transf --config=T1_2_MNI152_2mm
> applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm
--in=aparc+aseg.nii.gz --warp=my_nonlinear_transf --out=my_warped_structural


Best,
QZ
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[Freesurfer] intensity statistics in aseg.stats

[Zeng, Qi]

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Hi Freesurfer scholars,

The output of recon-all "aseg.stats" file contains information on volume
and intensity statistics of each segmentation of subcortical brain regions.
May I ask what is this intensity measurement (e.g. intensity mean)? How is
it different from volume? What characteristics of the brain did it try to
explain?
Thank you!

Best,
QZ
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Re: [Freesurfer] meanings of trac-all outputs

[Zeng, Qi]

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Hi Freesurfer experts,

Follow up on the last question and correct me if I am wrong, the difference
between dlabel/diff/lowb_brain_mask.nii.gz and dmri/nodif_brain_mask.nii.gz
is that:
> the dlabel/diff/lowb_brain_mask.nii.gz is generated from "bet" (brain
extraction)
> and dmri/nodif_brain_mask.nii is derived from aparc+aseg_mask.nii.gz
which contains T1 information.
Because in fsl, nodif_brain_mask is named for "bet binary brain mask".

Best,
Qi

Best,
Qi

On Fri, Apr 22, 2022 at 3:25 PM Zeng, Qi  wrote:

> Hi experts,
>
> Just want to check if dmri/dwi.nii.gz is the 4D dwi volumes after
> correction for B0 inhomogeneities, eddy current, and head motion? and
> dmri/nodif_brain_mask.nii.gz is the 3D ROI mask for the whole brain? and
> dmri/bvals and dmri/bvecs are rotated bvals and rotated bvecs?
> Thank you!
>
> Best,
> Qi
>


-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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[Freesurfer] meanings of trac-all outputs

[Zeng, Qi]

External Email - Use Caution

Hi experts,

Just want to check if dmri/dwi.nii.gz is the 4D dwi volumes after
correction for B0 inhomogeneities, eddy current, and head motion? and
dmri/nodif_brain_mask.nii.gz is the 3D ROI mask for the whole brain? and
dmri/bvals and dmri/bvecs are rotated bvals and rotated bvecs?
Thank you!

Best,
Qi
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[Freesurfer] mri_cor2label --surf "dim mismatch between surface"

[Zeng, Qi]

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Hi,

I saw the same question has been asked and no answer was provided:
I run
   "mri_cor2label --c fsaverage/mri/aseg.mgz --id 4 --l
fsaverage/label/Left-Lateral-Ventricle.label --surf fsaverage lh"-
to hopefully extract lateral ventricles volume into a overlay of surface
base. however, gave me error: "dim mismatch between surface (100515) and
input (16777216)".  What should I change?

BTW, Also have questions for the following steps and hope you can answer
that too:
1. convert surface-based label to volume,
"mri_label2vol --label fsaverage/label/Left-Lateral-Ventricle.label
--subject fsaverage --hemi lh --identify --temp fsaverage/mri/T1.mgz --o
fsaverage/mri/lh.Left-Lateral-Ventricle.nii --proj frac 0 1 0.01
2. Better ROI with mri_binarize
"mri_binarize" --dilate 1 -erode 1 --i
fsaverage/mri/h.Left-Lateral-Ventricle.nii --o
fsaverage/mri/h.Left-Lateral-Ventricle.nii --min 1
3. constrain the thick ROI
"mris_calc -o fsaverage/mri/h.Left-Lateral-Ventricle.nii
fsaverage/mri/h.Left-Lateral-Ventricle.nii  mul
fsaverage/mri/h.Left-Lateral-Ventricle.ribbon.mgz
4. Questions: Are the aforementioned steps correct?  In the end, if I have
a couple of ROIs, what should I use to combine them. or just load them
separately with lh.white and lh.pial.

Best,
Qi
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[Freesurfer] questions of tracula group analysis, freeview and pair analysis

[Zeng, Qi]

External Email - Use Caution

Hi,

I got a couple of questions regarding group analysis of tracula with a
longitudinal pipeline, freeview output heatmap key, and pair analysis's
fsgd & correction analysis.

1). I followed FsTutorial/TraculaStatistics - Free Surfer Wiki (harvard.edu)

 to
conduct a GLM group analysis for tracula results. But for the first step,
should I conduct a long_mris_slopes to get the rate of change just as
surface-based analysis for a longitudinal pipeline?

2). I tried freeview my sig.mgh results both for positive and negative for
my surface group analysis, is there a heatmap key I can put into the image
or available to export?

3). I created the FSDG file for pair analysis as follows to indicate both
the same and difference within the pair subject to hope to regress out the
effect of age at baseline and time_diff between subjects, is that the
correct way of formatting? and also how to create the subject name here if
my previous FSDG is sub01_ses-1.long.sub01_base and
sub01_ses-2.long.sub01_base for the subject name.

> GroupDescriptorFile 1
> Class Main
> Variables Age_bl Time_diff
> Input sub01pair   Main 30  7.1
> Input sub02pair   Main 40  2.2
> Input sub03pair   Main 50  3.7
> Input sub04pair   Main 60  0.7


4). Even not indicated in the pair analysis page, a cluster correction
"mri_glmfit-sim" is also necessary for the last step, right?

Thank you so much!


Best,

Qi
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Re: [Freesurfer] Freeview grey matter, white matter and Tracula outputs

[Zeng, Qi]

External Email - Use Caution

Hi Anastasia,

I tried to visualize the RD.nii with the following steps, however, it
doesn't represent well as fa.nii does. (attached below).

1) RD = (L2+L3)/2:  fslmaths dtifit_L2.nii -add dtifit_L3 -div 2
dtifit_RD.nii
2) mri_vol2vol --mov dmri/lowb.nii --targ mri/wmparc.mgz --inv --interp
nearest --o mri/wmparc2diff.mgz --reg dmri/xfms/anatorig2diff.bbr.dat
--no-save-reg
3) mri_mask dmri/dtifit_RD.nii mri/wmparc2diff.mgz dmri/rd-masked.mgz
4) freeview -v dmri/dtifit_RD.nii dmri/rd-masked.mgz

If I tried to color-code every diffusivity (rd, ad, fa), I failed by adding
"edgecolor=red(blue, or yellow)" following, what are the other options?
>> freeview -v
dmri/dtifit_FA.nii:reg=dmri/xfms/anatorig2diff.bbr.dat:edgecolor=red
dmri/dtifit_AD.nii:reg=dmri/xfms/anatorig2diff.bbr.dat:edgecolor=yellow...

FA.nii RD.nii
[image: FA2.JPG]   [image: RD1.JPG]

Thank you!
Best,
Jackie


On Mon, Nov 22, 2021 at 7:27 PM Yendiki, Anastasia 
wrote:

> See "viewing volumes with freeview" in the tutorial:
> https://secure-web.cisco.com/10RdLE2TlyCn6SHIX3mLEiv_Rt4eMDoWoVQI8x2WCLgHYOa_iLiVbEWCPrqo_upK5pKEjdYo4aplg-HRrqRzkfaEU_al0iK2OECP2ZDTv1MdzA-1XnxchLz01JlwyrBgo4ZPonKuAW2xhvQOPWu1liRgGByG2MAoysHLT3mT6QRtCorydcHq0Q5y0XLTF4j0rT1wcrX4MftxWKKCRJi8vgedQAINiadMWOTPdKCll_s7C2Yj0EGncoF91UYoSYejTVTLGEzKLM4KJt_yRRjBZL5E3on8rtcjtgTH7hUKJoyEBlS6bbjht2prEJO4nBWiz/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview
>
> When you view the aseg, aparc+aseg, or any other FreeSurfer segmentation
> volume, make sure that the colormap is not grayscale but "look-up table".
>
> You can get the AD and RD from the other outputs:
> AD = L1
> RD = (L2+L3)/2
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, November 22, 2021 5:24 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Freeview grey matter, white matter and Tracula
> outputs
>
>
> External Email - Use Caution
>
> Hi,
>
> If I want to freeview fully segmented grey matter, white matter, and
> Tracula outputs, are the following commands correct to the request?
>
> # to visualize the segmented cortical outputs
> freeview -v mri/aparc+aseg.mgz
> Question: why is one hemisphere brighter than the other? How can I adjust
> so that they are equally bright?
>
> # to visualize the segmented subcortical outputs
> freeview -v mri/aseg.mgz
> Question: why is only one hemisphere showing and how to add the other one?
>
> $ to visualize AD. RD, FA and color-coded each
> freeview -v dmri/dtifit_FA.nii
> Question: I cannot find the nifti outputs of AD and RD (however, the stats
> generated). where can I find it? Is there an example of how to color-code
> them for freeview?
>
> Thank you!
> Best,
> Jackie
> ___
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-- 

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Icahn School of Medicine at Mount Sinai
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[Freesurfer] Freeview grey matter, white matter and Tracula outputs

[Zeng, Qi]

External Email - Use Caution

Hi,

If I want to freeview fully segmented grey matter, white matter, and
Tracula outputs, are the following commands correct to the request?

# to visualize the segmented cortical outputs
freeview -v mri/aparc+aseg.mgz
Question: why is one hemisphere brighter than the other? How can I adjust
so that they are equally bright?

# to visualize the segmented subcortical outputs
freeview -v mri/aseg.mgz
Question: why is only one hemisphere showing and how to add the other one?

$ to visualize AD. RD, FA and color-coded each
freeview -v dmri/dtifit_FA.nii
Question: I cannot find the nifti outputs of AD and RD (however, the stats
generated). where can I find it? Is there an example of how to color-code
them for freeview?

Thank you!
Best,
Jackie
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Re: [Freesurfer] register.dat

[Zeng, Qi]

External Email - Use Caution

Sorry for the trouble, I seemed to find the registration matrix located in
xfms/anatorig2diff.bbr.dat. Is that one correct?

Best,
Jackie



On Mon, Nov 22, 2021 at 12:36 PM Zeng, Qi  wrote:

> Hi Experts,
>
> My tracula completed with no error. So I was trying to view the fa.nii
> with the following command:
> freeview -v mri/brain.mgz  mri/orig.mgz
> mri/wmparc.mgz:colormap=lut:opacity=0.2
> dmri/dtifit_FA.nii:reg=touch/rusage.mri_ca_register.dat:colormap=heat:heatscale=.2,.2,1
> -colorscale -viewport coronal.
>
> It returned with an error message saying: "reading registration failed". I
> have looked at the register.dat from the following link: RegisterDat -
> Free Surfer Wiki (harvard.edu)
> <https://secure-web.cisco.com/1lq63fsRRr9_zp2-PjLm-4XE_tgI707ZrZ0h6aNNJxE32zm70v33X7HR2P6mUpPYNhDLq_OqGUFN0G3I62daXUX3T4AMW7dKWJfaXfmWgQ85VJ1cE-sxz1JsnMLSuLxqt3sVst-tuu4IkX86REI72fghEKSxzyLiP-xAN2djRAHxTjrQyl_4GYHFEUvh7Zo1pM75IRxQ_QvS8RbAL5ypgqK9X6hLXVZx66xOf1T16pFtqtwAEJmtWkUNhlxN5QMLv06Kj1RsVcoTSD_VdXsC1jA9_fcsZSGB_Az23CpkF-Mz-pTZ-yfoaZGX1WaQgsmIaiv6CQGEbWiQE86RICJd93Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRegisterDat>.
>  My register.dat
> is nothing like that (attached below). So where should the file locate?
>
> Best,
> Jackie
>
>
>

-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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[Freesurfer] register.dat

[Zeng, Qi]

External Email - Use Caution

Hi Experts,

My tracula completed with no error. So I was trying to view the fa.nii with
the following command:
freeview -v mri/brain.mgz  mri/orig.mgz
mri/wmparc.mgz:colormap=lut:opacity=0.2
dmri/dtifit_FA.nii:reg=touch/rusage.mri_ca_register.dat:colormap=heat:heatscale=.2,.2,1
-colorscale -viewport coronal.

It returned with an error message saying: "reading registration failed". I
have looked at the register.dat from the following link: RegisterDat - Free
Surfer Wiki (harvard.edu)
.
 My register.dat is
nothing like that (attached below). So where should the file locate?

Best,
Jackie


rusage.mri_ca_register.dat
Description: Binary data
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Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

For example, if my Class CaseFemaleNonWhite has no subject, should I cancel
the contrast between CaseFemaleNonWhite vs ControlFemaleNonWhite?
However, that will leave my ControlFemaleNonWhite subjects unrecognized? Or
it is better to cancel the race discrete as covariates?

Best,
Zeng


On Thu, Nov 11, 2021 at 4:07 PM Zeng, Qi  wrote:

> got you, thanks
>
> Best,
> Zeng
>
>
>
> On Thu, Nov 11, 2021 at 4:06 PM Douglas N. Greve 
> wrote:
>
>> For DODS you would add 16 zeros (8 classes times 2 continuous variables)
>>
>> On 11/11/2021 4:00 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> So for the DODS case, is "1 -1 1 -1 1 -1 1 -1 0 0 0 0" for the following
>> FSGD:
>>
>> GroupDescriptorFile 1
>> Title MyStudy
>> Class CaseMaleWhite
>> Class ControlMaleWhite
>> Class CaseMaleNonWhite
>> Class ControlMaleNonWhite
>> Class CaseFemaleWhite
>> Class ControlFemaleWhite
>> Class CaseFemaleNonWhite
>> Class ControlFemaleNonWhite
>> Variables age_bl eTIV
>> Input Sub001_base ControlFemaleWhite 85 1350519.71
>> Input Sub002_base ControlFemaleWhite 81.3 1558515.86
>>
>> Best,
>> Qi
>>
>> On Thu, Nov 11, 2021 at 3:28 PM Douglas N. Greve 
>> wrote:
>>
>>> For the DOSS case, yes.
>>>
>>> On 11/11/2021 3:23 PM, Zeng, Qi wrote:
>>>
>>> External Email - Use Caution
>>> Hi  Douglas,
>>>
>>> If to set up the FSGD as below, is my design matrix for case and control
>>> comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?
>>>
>>> GroupDescriptorFile 1
>>> Title MyStudy
>>> Class CaseMaleWhite
>>> Class ControlMaleWhite
>>> Class CaseMaleNonWhite
>>> Class ControlMaleNonWhite
>>> Class CaseFemaleWhite
>>> Class ControlFemaleWhite
>>> Class CaseFemaleNonWhite
>>> Class ControlFemaleNonWhite
>>> VariablesAge eTIV
>>> Input Sub001_base  Control   Female  White   85 1350519.71
>>> Input Sub002_base  Control   Female  White   81.3   1558515.86
>>>
>>> Best,
>>> Qi
>>>
>>> On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve 
>>> wrote:
>>>
>>>> I would advice setting up the FSGD files with 8 classes based on your 3
>>>> discrete, 2-level variables, eg, MaleControlWhite then use two continuous
>>>> variables Age and eTIV.
>>>> You should definitely normalize the eTIV (and probably age too)
>>>>
>>>> On 11/10/2021 7:07 PM, Zeng, Qi wrote:
>>>>
>>>> External Email - Use Caution
>>>> Hi Douglas,
>>>>
>>>> Just to be clear, should I recode discrete variables as numeric as
>>>> sample1) or change discrete variables into strings 2) or even change the
>>>> comparison groups into strings too 3)?
>>>> 1)
>>>> Variables Age Gender Race eTIV
>>>> Input Sub001_base Control 85 1 1 1350519.71
>>>> Input Sub002_base Control 81.3   0 1 1558515.86
>>>> Input Sub003_base Control 81.3   0 0 1558515.86
>>>>
>>>> or 2)
>>>> Variables Age Gender Race eTIV
>>>> Input Sub001_base Control 85 "Female" "White" 1350519.71
>>>> Input Sub002_base Control 81.3  "Male" "White" 1558515.86
>>>> Input Sub003_base Control 72.7  "Male" "White" 1187649.47
>>>>
>>>> or 3)
>>>> Variables  Age Gender Race eTIV
>>>> Input Sub001_base "Control" 85 "Female" "White" 1350519.71
>>>> Input Sub002_base "Control" 81.3  "Male" "White" 1558515.86
>>>> Input Sub003_base "Control" 72.7  "Male" "White" 1187649.47
>>>>
>>>>
>>>> Best,
>>>> Zeng
>>>>
>>>>
>>>>
>>>> On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve <
>>>> dgr...@mgh.harvard.edu> wrote:
>>>>
>>>>> Did you read the error message? It says:
>>>>> Variable 2 has character string Female
>>>>> Variables should be continuous numbers
>>>>> You have listed Gender and Race as strings, they have to be numbers
>>>>> (eg, 1, 2)
>>>>> You probably want to have these be discrete variables instead of
>>>>> continuous
>>>>>
>>>&

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

got you, thanks

Best,
Zeng



On Thu, Nov 11, 2021 at 4:06 PM Douglas N. Greve 
wrote:

> For DODS you would add 16 zeros (8 classes times 2 continuous variables)
>
> On 11/11/2021 4:00 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> So for the DODS case, is "1 -1 1 -1 1 -1 1 -1 0 0 0 0" for the following
> FSGD:
>
> GroupDescriptorFile 1
> Title MyStudy
> Class CaseMaleWhite
> Class ControlMaleWhite
> Class CaseMaleNonWhite
> Class ControlMaleNonWhite
> Class CaseFemaleWhite
> Class ControlFemaleWhite
> Class CaseFemaleNonWhite
> Class ControlFemaleNonWhite
> Variables age_bl eTIV
> Input Sub001_base ControlFemaleWhite 85 1350519.71
> Input Sub002_base ControlFemaleWhite 81.3 1558515.86
>
> Best,
> Qi
>
> On Thu, Nov 11, 2021 at 3:28 PM Douglas N. Greve 
> wrote:
>
>> For the DOSS case, yes.
>>
>> On 11/11/2021 3:23 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> Hi  Douglas,
>>
>> If to set up the FSGD as below, is my design matrix for case and control
>> comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?
>>
>> GroupDescriptorFile 1
>> Title MyStudy
>> Class CaseMaleWhite
>> Class ControlMaleWhite
>> Class CaseMaleNonWhite
>> Class ControlMaleNonWhite
>> Class CaseFemaleWhite
>> Class ControlFemaleWhite
>> Class CaseFemaleNonWhite
>> Class ControlFemaleNonWhite
>> VariablesAge eTIV
>> Input Sub001_base  Control   Female  White   85 1350519.71
>> Input Sub002_base  Control   Female  White   81.3   1558515.86
>>
>> Best,
>> Qi
>>
>> On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve 
>> wrote:
>>
>>> I would advice setting up the FSGD files with 8 classes based on your 3
>>> discrete, 2-level variables, eg, MaleControlWhite then use two continuous
>>> variables Age and eTIV.
>>> You should definitely normalize the eTIV (and probably age too)
>>>
>>> On 11/10/2021 7:07 PM, Zeng, Qi wrote:
>>>
>>> External Email - Use Caution
>>> Hi Douglas,
>>>
>>> Just to be clear, should I recode discrete variables as numeric as
>>> sample1) or change discrete variables into strings 2) or even change the
>>> comparison groups into strings too 3)?
>>> 1)
>>> Variables Age Gender Race eTIV
>>> Input Sub001_base Control 85 1 1 1350519.71
>>> Input Sub002_base Control 81.3   0 1 1558515.86
>>> Input Sub003_base Control 81.3   0 0 1558515.86
>>>
>>> or 2)
>>> Variables Age Gender Race eTIV
>>> Input Sub001_base Control 85 "Female" "White" 1350519.71
>>> Input Sub002_base Control 81.3  "Male" "White" 1558515.86
>>> Input Sub003_base Control 72.7  "Male" "White" 1187649.47
>>>
>>> or 3)
>>> Variables  Age Gender Race eTIV
>>> Input Sub001_base "Control" 85 "Female" "White" 1350519.71
>>> Input Sub002_base "Control" 81.3  "Male" "White" 1558515.86
>>> Input Sub003_base "Control" 72.7  "Male" "White" 1187649.47
>>>
>>>
>>> Best,
>>> Zeng
>>>
>>>
>>>
>>> On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve 
>>> wrote:
>>>
>>>> Did you read the error message? It says:
>>>> Variable 2 has character string Female
>>>> Variables should be continuous numbers
>>>> You have listed Gender and Race as strings, they have to be numbers
>>>> (eg, 1, 2)
>>>> You probably want to have these be discrete variables instead of
>>>> continuous
>>>>
>>>> On 11/10/2021 6:20 PM, Zeng, Qi wrote:
>>>>
>>>> External Email - Use Caution
>>>> Hi Douglas,
>>>>
>>>> Here is the command line:
>>>> mri_glmfit \
>>>>   --y rh.thickness-rate.MyStudy.10.mgh \
>>>>   --fsgd FSGD/MyStudy.fsgd dods\
>>>>   --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
>>>>   --surf fsaverage rh \
>>>>   --cortex \
>>>>   --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir
>>>> \
>>>>   --eres-save
>>>>
>>>> Also error message in terminal:
>>>> gdfRead(): reading FSGD/MyStudy.fsgd
>>>> WARNING: variable 1 is "Gender" which is often a discrete factor
>>>&g

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

So for the DODS case, is "1 -1 1 -1 1 -1 1 -1 0 0 0 0" for the following
FSGD:

GroupDescriptorFile 1
Title MyStudy
Class CaseMaleWhite
Class ControlMaleWhite
Class CaseMaleNonWhite
Class ControlMaleNonWhite
Class CaseFemaleWhite
Class ControlFemaleWhite
Class CaseFemaleNonWhite
Class ControlFemaleNonWhite
Variables age_bl eTIV
Input Sub001_base ControlFemaleWhite 85 1350519.71
Input Sub002_base ControlFemaleWhite 81.3 1558515.86

Best,
Qi

On Thu, Nov 11, 2021 at 3:28 PM Douglas N. Greve 
wrote:

> For the DOSS case, yes.
>
> On 11/11/2021 3:23 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi  Douglas,
>
> If to set up the FSGD as below, is my design matrix for case and control
> comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?
>
> GroupDescriptorFile 1
> Title MyStudy
> Class CaseMaleWhite
> Class ControlMaleWhite
> Class CaseMaleNonWhite
> Class ControlMaleNonWhite
> Class CaseFemaleWhite
> Class ControlFemaleWhite
> Class CaseFemaleNonWhite
> Class ControlFemaleNonWhite
> VariablesAge eTIV
> Input Sub001_base  Control   Female  White   85 1350519.71
> Input Sub002_base  Control   Female  White   81.3   1558515.86
>
> Best,
> Qi
>
> On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve 
> wrote:
>
>> I would advice setting up the FSGD files with 8 classes based on your 3
>> discrete, 2-level variables, eg, MaleControlWhite then use two continuous
>> variables Age and eTIV.
>> You should definitely normalize the eTIV (and probably age too)
>>
>> On 11/10/2021 7:07 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> Hi Douglas,
>>
>> Just to be clear, should I recode discrete variables as numeric as
>> sample1) or change discrete variables into strings 2) or even change the
>> comparison groups into strings too 3)?
>> 1)
>> Variables Age Gender Race eTIV
>> Input Sub001_base Control 85 1 1 1350519.71
>> Input Sub002_base Control 81.3   0 1 1558515.86
>> Input Sub003_base Control 81.3   0 0 1558515.86
>>
>> or 2)
>> Variables Age Gender Race eTIV
>> Input Sub001_base Control 85 "Female" "White" 1350519.71
>> Input Sub002_base Control 81.3  "Male" "White" 1558515.86
>> Input Sub003_base Control 72.7  "Male" "White" 1187649.47
>>
>> or 3)
>> Variables  Age Gender Race eTIV
>> Input Sub001_base "Control" 85 "Female" "White" 1350519.71
>> Input Sub002_base "Control" 81.3  "Male" "White" 1558515.86
>> Input Sub003_base "Control" 72.7  "Male" "White" 1187649.47
>>
>>
>> Best,
>> Zeng
>>
>>
>>
>> On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve 
>> wrote:
>>
>>> Did you read the error message? It says:
>>> Variable 2 has character string Female
>>> Variables should be continuous numbers
>>> You have listed Gender and Race as strings, they have to be numbers (eg,
>>> 1, 2)
>>> You probably want to have these be discrete variables instead of
>>> continuous
>>>
>>> On 11/10/2021 6:20 PM, Zeng, Qi wrote:
>>>
>>> External Email - Use Caution
>>> Hi Douglas,
>>>
>>> Here is the command line:
>>> mri_glmfit \
>>>   --y rh.thickness-rate.MyStudy.10.mgh \
>>>   --fsgd FSGD/MyStudy.fsgd dods\
>>>   --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
>>>   --surf fsaverage rh \
>>>   --cortex \
>>>   --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \
>>>   --eres-save
>>>
>>> Also error message in terminal:
>>> gdfRead(): reading FSGD/MyStudy.fsgd
>>> WARNING: variable 1 is "Gender" which is often a discrete factor
>>>   The proper way to handle discrete factors is to create classes.
>>>   See *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1YCu4DNGxoLi5zalwi9XfWKMLYA4OOBRYPZEzRdP4RJSWFg4O4d3dLnnPVas8EHBUxfF4nSV-eC7ZFjIN1sY2rJwXO6iZ4xxPfGVfmY32_enNyymSd3OE8kX7WuqFkJwiPWLJf_BqmMMblUXJq5g8qaoRcoLASZyTMIRk13_MSQzmFbs1aA9JiImnKzvAUs6x74pkeHZFb9HR8i-1t7qcTREdnjKp7auywSjuJlcwgX31jHP0UBL2NTjFB5ExlTb8pXoNrXjeK7kegis1cJKEHt-qnLP2MROMOUN6pRnNwXi4MXcheqatZ6jHhynNPW-G/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>>> <https://secure-web.cisco.com/1NHVxBIRnha6EjEdEho81-VE9d-vjJ6ivzt10z28vhX9c94pCwosQpkLG4Hfu3nLYp7KMDne5wAk9mK45YIQJEZBe6UlteF2

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

Hi  Douglas,

If to set up the FSGD as below, is my design matrix for case and control
comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?

GroupDescriptorFile 1
Title MyStudy
Class CaseMaleWhite
Class ControlMaleWhite
Class CaseMaleNonWhite
Class ControlMaleNonWhite
Class CaseFemaleWhite
Class ControlFemaleWhite
Class CaseFemaleNonWhite
Class ControlFemaleNonWhite
VariablesAge eTIV
Input Sub001_base  Control   Female  White   85 1350519.71
Input Sub002_base  Control   Female  White   81.3   1558515.86

Best,
Qi

On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve 
wrote:

> I would advice setting up the FSGD files with 8 classes based on your 3
> discrete, 2-level variables, eg, MaleControlWhite then use two continuous
> variables Age and eTIV.
> You should definitely normalize the eTIV (and probably age too)
>
> On 11/10/2021 7:07 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Just to be clear, should I recode discrete variables as numeric as
> sample1) or change discrete variables into strings 2) or even change the
> comparison groups into strings too 3)?
> 1)
> Variables Age Gender Race eTIV
> Input Sub001_base Control 85 1 1 1350519.71
> Input Sub002_base Control 81.3   0 1 1558515.86
> Input Sub003_base Control 81.3   0 0 1558515.86
>
> or 2)
> Variables Age Gender Race eTIV
> Input Sub001_base Control 85 "Female" "White" 1350519.71
> Input Sub002_base Control 81.3  "Male" "White" 1558515.86
> Input Sub003_base Control 72.7  "Male" "White" 1187649.47
>
> or 3)
> Variables  Age Gender Race eTIV
> Input Sub001_base "Control" 85 "Female" "White" 1350519.71
> Input Sub002_base "Control" 81.3  "Male" "White" 1558515.86
> Input Sub003_base "Control" 72.7  "Male" "White" 1187649.47
>
>
> Best,
> Zeng
>
>
>
> On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve 
> wrote:
>
>> Did you read the error message? It says:
>> Variable 2 has character string Female
>> Variables should be continuous numbers
>> You have listed Gender and Race as strings, they have to be numbers (eg,
>> 1, 2)
>> You probably want to have these be discrete variables instead of
>> continuous
>>
>> On 11/10/2021 6:20 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> Hi Douglas,
>>
>> Here is the command line:
>> mri_glmfit \
>>   --y rh.thickness-rate.MyStudy.10.mgh \
>>   --fsgd FSGD/MyStudy.fsgd dods\
>>   --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
>>   --surf fsaverage rh \
>>   --cortex \
>>   --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \
>>   --eres-save
>>
>> Also error message in terminal:
>> gdfRead(): reading FSGD/MyStudy.fsgd
>> WARNING: variable 1 is "Gender" which is often a discrete factor
>>   The proper way to handle discrete factors is to create classes.
>>   See *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1NEzix1p8cerzV2CscGJeOM5AxEOJi5zLORLiOeZ2wx-E6_vkK5NJqo-ry86kD_ktTitKimPz89haZ5YiKI_4QFVeWpS_2FVRxv4v08GpB0KFONvbcMNu8gXJXWC1jH0EgCJB7TExvThbl-TrnJRXNC9DL6fkI1EjUkdxMF1vblej9_5Js9YfDFO0Sm0_Dm7riTKQRk1rWAukdd7DQPVqsESboEgslbaclvRlzo-WERzaRjKLPE7OLHKD32WuHtT_tN0UAKlbTKFCXPm_ensblo6QhQDJnafIGxdB_3EqzyQZls7VQX1kP6qEE6XoXXIHmltlroSNZgmBMQofEYUMkg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>> <https://secure-web.cisco.com/1NHVxBIRnha6EjEdEho81-VE9d-vjJ6ivzt10z28vhX9c94pCwosQpkLG4Hfu3nLYp7KMDne5wAk9mK45YIQJEZBe6UlteF2wwLohmZJzp070UjHvv6fqugRAkgBk0uNO3Fsgo5BzblW95J5iO5sXWwZLK-LGAZJJTBaU7mLTkO5L70JRSscCW3pdc-G5KchZMbVyeY65gGH4w5MMIYBSVHvX03spMjZ85XkHbkgYYmWXTFnzqUGhqGgHygP5sLeR7OWPKIzEb7X3pHi7POf0UyEHJAZpQLU9bgT2BnOcClt0kW4mll1ODQDC2Y0U7-0f/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples>
>> ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base
>>  Variable 2 has character string Female
>>  Variables should be continuous numbers
>> FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input
>>
>> Also attached FSGD file below.
>> Thank you so much for the help!
>>
>> Best,
>> Zeng
>>
>>
>>
>>
>> On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve 
>> wrote:
>>
>>> please send your command line and full terminal output as well as the
>>> fsgd file
>>>
>>> On 11/10/2021 5:12 PM, Zeng, Qi wrote:
>>>
>>> External Email - Use

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

Hi Douglas,

Just to be clear, should I recode discrete variables as numeric as sample1)
or change discrete variables into strings 2) or even change the comparison
groups into strings too 3)?
1)
Variables Age Gender Race eTIV
Input Sub001_base Control 85 1 1 1350519.71
Input Sub002_base Control 81.3   0 1 1558515.86
Input Sub003_base Control 81.3   0 0 1558515.86

or 2)
Variables Age Gender Race eTIV
Input Sub001_base Control 85 "Female" "White" 1350519.71
Input Sub002_base Control 81.3  "Male" "White" 1558515.86
Input Sub003_base Control 72.7  "Male" "White" 1187649.47

or 3)
Variables  Age Gender Race eTIV
Input Sub001_base "Control" 85 "Female" "White" 1350519.71
Input Sub002_base "Control" 81.3  "Male" "White" 1558515.86
Input Sub003_base "Control" 72.7  "Male" "White" 1187649.47


Best,
Zeng



On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve 
wrote:

> Did you read the error message? It says:
> Variable 2 has character string Female
> Variables should be continuous numbers
> You have listed Gender and Race as strings, they have to be numbers (eg,
> 1, 2)
> You probably want to have these be discrete variables instead of continuous
>
> On 11/10/2021 6:20 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Here is the command line:
> mri_glmfit \
>   --y rh.thickness-rate.MyStudy.10.mgh \
>   --fsgd FSGD/MyStudy.fsgd dods\
>   --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
>   --surf fsaverage rh \
>   --cortex \
>   --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \
>   --eres-save
>
> Also error message in terminal:
> gdfRead(): reading FSGD/MyStudy.fsgd
> WARNING: variable 1 is "Gender" which is often a discrete factor
>   The proper way to handle discrete factors is to create classes.
>   See *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1wooLw3zkqSmNDmxJNAdL3vHs5YqXnNqVwhC-ElE-BfUuDbqvyhpqGlkSnckR-Ri3BITTwfry6sCZv76ek-tpOsw4o-yGa_G9o5NpsCmoDKTjoC5oRtbp_z1fxPzJjOwriNnWF_sNs5bf6-tAKyygUTgCWfDnQyJ87CkTsquI8kwqoMFNasAVhbSV8BqaK78yDF_Iv0vrp8xRngyE5zmYZZeMy8wRJwY1s6Bpw9J8cEXc8Z3UUP0WbfRMO1d15k8cdBtnBld667_GWXuj3YfnX210nWSevRup0W1Nbmc3CESOrQ9VSSfGJfov53bZD8_ZWR40DzOBJXqtCFa0u50Hrg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
> <https://secure-web.cisco.com/1NHVxBIRnha6EjEdEho81-VE9d-vjJ6ivzt10z28vhX9c94pCwosQpkLG4Hfu3nLYp7KMDne5wAk9mK45YIQJEZBe6UlteF2wwLohmZJzp070UjHvv6fqugRAkgBk0uNO3Fsgo5BzblW95J5iO5sXWwZLK-LGAZJJTBaU7mLTkO5L70JRSscCW3pdc-G5KchZMbVyeY65gGH4w5MMIYBSVHvX03spMjZ85XkHbkgYYmWXTFnzqUGhqGgHygP5sLeR7OWPKIzEb7X3pHi7POf0UyEHJAZpQLU9bgT2BnOcClt0kW4mll1ODQDC2Y0U7-0f/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples>
> ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base
>  Variable 2 has character string Female
>  Variables should be continuous numbers
> FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input
>
> Also attached FSGD file below.
> Thank you so much for the help!
>
> Best,
> Zeng
>
>
>
>
> On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve 
> wrote:
>
>> please send your command line and full terminal output as well as the
>> fsgd file
>>
>> On 11/10/2021 5:12 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> Hi Freesurfer experts,
>>
>> Here, I want to design a simple group comparison (two levels: Case vs.
>> Control) and also count for 4 covariates (two continuous and two
>> categoricals). However, the GLM model cannot recognize my discrete
>> variables. What do you suggest to change?
>> >> FSDG file:
>> GroupDescriptorFile 1
>> Title MyStudy
>> Class Control
>> Class Case
>> Variables age gender race  eTIV
>> Input sub001_base Control 85 Female White 1350519
>> Contrast:
>> >> Design matrix for Case-Control and regress out the effect of age,
>> gender, race, and eTIV.
>> -1 1 0 0 0 0 0 0 0 0
>>
>> Best,
>> Zeng
>>
>>
>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1riDKYS-FGseRCaBPDFbfM10KeLQ0kNrmsbKoEpOzznltcGj9v-5n_mtcH4iuPpyQdPnJpDqv2oznuvHcCG0AoePAHtplLU3aqtaLbpH7r9l72LUZMShuoVRoexJpk22Z0KJ4UF-qkQIfw_bIfhHlkLc9H1-DLhctPeXE_toredYS7-4qs-W0QxiUq1kBtbAmLnJmze-ioLsfDBZDMhUGZSIqNcc_nJSQEFuPObCRfGVv7Y

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

Hi Douglas,

Here is the command line:
mri_glmfit \
  --y rh.thickness-rate.MyStudy.10.mgh \
  --fsgd FSGD/MyStudy.fsgd dods\
  --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
  --surf fsaverage rh \
  --cortex \
  --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \
  --eres-save

Also error message in terminal:
gdfRead(): reading FSGD/MyStudy.fsgd
WARNING: variable 1 is "Gender" which is often a discrete factor
  The proper way to handle discrete factors is to create classes.
  See 
https://secure-web.cisco.com/1NHVxBIRnha6EjEdEho81-VE9d-vjJ6ivzt10z28vhX9c94pCwosQpkLG4Hfu3nLYp7KMDne5wAk9mK45YIQJEZBe6UlteF2wwLohmZJzp070UjHvv6fqugRAkgBk0uNO3Fsgo5BzblW95J5iO5sXWwZLK-LGAZJJTBaU7mLTkO5L70JRSscCW3pdc-G5KchZMbVyeY65gGH4w5MMIYBSVHvX03spMjZ85XkHbkgYYmWXTFnzqUGhqGgHygP5sLeR7OWPKIzEb7X3pHi7POf0UyEHJAZpQLU9bgT2BnOcClt0kW4mll1ODQDC2Y0U7-0f/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base
 Variable 2 has character string Female
 Variables should be continuous numbers
FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input

Also attached FSGD file below.
Thank you so much for the help!

Best,
Zeng




On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve 
wrote:

> please send your command line and full terminal output as well as the fsgd
> file
>
> On 11/10/2021 5:12 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Freesurfer experts,
>
> Here, I want to design a simple group comparison (two levels: Case vs.
> Control) and also count for 4 covariates (two continuous and two
> categoricals). However, the GLM model cannot recognize my discrete
> variables. What do you suggest to change?
> >> FSDG file:
> GroupDescriptorFile 1
> Title MyStudy
> Class Control
> Class Case
> Variables age gender race  eTIV
> Input sub001_base Control 85 Female White 1350519
> Contrast:
> >> Design matrix for Case-Control and regress out the effect of age,
> gender, race, and eTIV.
> -1 1 0 0 0 0 0 0 0 0
>
> Best,
> Zeng
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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MyStudy.fsgd
Description: Binary data
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[Freesurfer] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

Hi Freesurfer experts,

Here, I want to design a simple group comparison (two levels: Case vs.
Control) and also count for 4 covariates (two continuous and two
categoricals). However, the GLM model cannot recognize my discrete
variables. What do you suggest to change?
>> FSDG file:
GroupDescriptorFile 1
Title MyStudy
Class Control
Class Case
Variables age gender race  eTIV
Input sub001_base Control 85 Female White 1350519
Contrast:
>> Design matrix for Case-Control and regress out the effect of age,
gender, race, and eTIV.
-1 1 0 0 0 0 0 0 0 0

Best,
Zeng
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Re: [Freesurfer] adding covariates to a longitudinal glmfit model

[Zeng, Qi]

External Email - Use Caution

Hi Freesurfer Experts,

Just a follow-up on the questions I asked last week and tested if the
questions get through to the list. Thanks for your help in advance!

Best,
Zeno

On Fri, Oct 29, 2021 at 10:39 PM Zeng, Qi  wrote:

> Hi Experts,
>
> After completing long_mris_slopes to get the rate of change and then
> concatenating them into one.mgh file for group analysis (mris_preproc). I
> am finally getting to mris_glmfit. Got a couple of questions along the way.
> 1). if I conducted long_mris_slopes, and got for example,
> lh.long.thickness-rate.fwhm10.fsaverage.mgh. Do I need to do a surface
> smoothing again (mri_surf2surf) before mris_glmfit?
> 2). I construct covariates in FSGD besides the group contrast that I am
> interested in. How do I add covariates into the glmfit model to control for
> the covariates as I contrast groups in terms of the rate of changing (CV
> vs. NCV groups) . Do I add them into --C as  (1, -1, 0(age), 0(gender),
> 0(race)).
> mri_glmfit
> --y {$hemi}.{$meas}-rate.{$smoothness}.mgh
> --fsgd FSGD/{$study}.fsgd doss
> --C Contrasts/CV-NCV.mtx(1, -1)
> --C Contrasts/NCV-CV.mtx (-1, 1)
> --surf fsaverage {$hemi}
> --cortex
> --glmdir {$hemi}.{$meas}-rate.{$study}.{$smoothness}.glmdir
>
>
> Best,
> Zeno
>
>
> --
>
>
>

-- 

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[Freesurfer] adding covariates to a longitudinal glmfit model

[Zeng, Qi]

External Email - Use Caution

Hi Experts,

After completing long_mris_slopes to get the rate of change and then
concatenating them into one.mgh file for group analysis (mris_preproc). I
am finally getting to mris_glmfit. Got a couple of questions along the way.
1). if I conducted long_mris_slopes, and got for example,
lh.long.thickness-rate.fwhm10.fsaverage.mgh. Do I need to do a surface
smoothing again (mri_surf2surf) before mris_glmfit?
2). I construct covariates in FSGD besides the group contrast that I am
interested in. How do I add covariates into the glmfit model to control for
the covariates as I contrast groups in terms of the rate of changing (CV
vs. NCV groups) . Do I add them into --C as  (1, -1, 0(age), 0(gender),
0(race)).
mri_glmfit
--y {$hemi}.{$meas}-rate.{$smoothness}.mgh
--fsgd FSGD/{$study}.fsgd doss
--C Contrasts/CV-NCV.mtx(1, -1)
--C Contrasts/NCV-CV.mtx (-1, 1)
--surf fsaverage {$hemi}
--cortex
--glmdir {$hemi}.{$meas}-rate.{$study}.{$smoothness}.glmdir


Best,
Zeno


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[Freesurfer] individual analysis and visualization

[Zeng, Qi]

External Email - Use Caution

Hi Experts,

If I want to analyze and visualize baseline and follow-up for an individual
subject's change (before-after & after-before).  Should I treat it as a
cross-sectional analysis for a group analysis?

Best,
Zeno
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[Freesurfer] visualizing regional significant correlation with clinical traits by group

[Zeng, Qi]

External Email - Use Caution

Hi Experts,

I've finished my run of generating volumetric and Tracula data for
subjects.  I was wondering if there is a way of displaying
significant regions that correlate with clinical traits and also by groups.
If there is a page describing this function, please help to share. I only
find knowledge about group analysis.
Thank you so much and I really appreciate it!

Best,
Qi
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[Freesurfer] qcache option for post recon-all longitudinal data

[Zeng, Qi]

External Email - Use Caution

Hi Freesurfer experts,

I've done running a longitudinal analysis pipeline for individuals in 3
groups. Now, I need to get prepared for QDEC group analysis. I cp all
groups of individuals to the same directory and each subject contains one
base and multiple long files. I want to run "-qcache" option for the prep.
Got a couple of questions here?
1) I failed to run "recon-all -s 001 -qcache", said: "missing
001/surf/lh.thickness", so for a longitudinal run, should I run "recon-all
-s 001_base -qcache" or 'recon-all -s 001_ses-1.long.001_base" instead?
2) Where will the output be stored for each individual?
3) To run multiple qcache in parallel, will the following code generate the
same outputs as that I run each individually: " find . -type d -name
'*_base" -exec bash -c 'for i in "$@"; do recon-all -s "$i" -qcache; done".
Thank you so much!

Best,
Qi
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Re: [Freesurfer] problem running last step longitudinal analysis

[Zeng, Qi]

External Email - Use Caution

Hi Douglas,

They each contained mri/norm.mgz.

Best,
Qi


On Tue, Apr 20, 2021 at 10:10 AM Douglas N. Greve 
wrote:

> and do they each have a norm.mgz?
>
> On 4/19/2021 4:11 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> I found the aseg.presurf.mgz for all cross sessions and base using version
> 6.0.
>
> Best,
> Qi
>
> On Sun, Apr 18, 2021 at 10:43 PM Douglas N. Greve 
> wrote:
>
>> Check each of your cross time points to make sure that all have an
>> aseg.presurf.mgz.
>>
>> On 4/16/2021 4:35 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> Hi Experts,
>>
>> I am running the last step (-long) for a longitudinal analysis, However,
>> encountering an error message saying: "error: ERROR: number of asegs and
>> norm volumes do not match" for all the subjects I run this time. A similar
>> problem has been reported before as the following link. The answer to the
>> question is 'Freesufer version too old'. I have been following the exact
>> same steps two months ago for my last cohort and it was fine. However, this
>> time all the subjects reporting error messages (attaching error.log).
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be* Re: [Freesurfer]
>> mri_fuse_segmentations error in longitudinal stream (mail-archive.com)
>> <https://secure-web.cisco.com/1xcCNPG6jeY7R3XZUuavTvtod8U5a5tYZLLrz9Kuekmq6urr93Pj9YlhGSs1R4EAWpq0dWFkeoXrGRBY_2OnG-FWOLEtpOIFlgMfrU9JOnTgsia94ixdd24hIoA9hBYXfx6QglgAsNEgAMz8ItLj_ICK-INdIrQgfeRFNE3DYaK0EPsWX6AZuFpxyX4i022yFit13vhaCidGQgkVtFuJzx5hig2Rwpj5bLkYhkS6v0DXbsQkLh5kHrA90mR0Ve6gSi6RyRjELElXiC9wHqpZ4Xw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg46002.html>
>> My system: x86_64 GNU/Linux
>> Freesufer version: freesurfer/6.0.0
>> attached the error.log
>>
>> Best,
>> Qi
>>
>>
>>
>>
>> ___
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>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
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>>  
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>
>
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
>
> ___
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Re: [Freesurfer] problem running last step longitudinal analysis

[Zeng, Qi]

External Email - Use Caution

Hi Douglas,

I found the aseg.presurf.mgz for all cross sessions and base using version
6.0.

Best,
Qi

On Sun, Apr 18, 2021 at 10:43 PM Douglas N. Greve 
wrote:

> Check each of your cross time points to make sure that all have an
> aseg.presurf.mgz.
>
> On 4/16/2021 4:35 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Experts,
>
> I am running the last step (-long) for a longitudinal analysis, However,
> encountering an error message saying: "error: ERROR: number of asegs and
> norm volumes do not match" for all the subjects I run this time. A similar
> problem has been reported before as the following link. The answer to the
> question is 'Freesufer version too old'. I have been following the exact
> same steps two months ago for my last cohort and it was fine. However, this
> time all the subjects reporting error messages (attaching error.log).
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be* Re: [Freesurfer]
> mri_fuse_segmentations error in longitudinal stream (mail-archive.com)
> <https://secure-web.cisco.com/1xcCNPG6jeY7R3XZUuavTvtod8U5a5tYZLLrz9Kuekmq6urr93Pj9YlhGSs1R4EAWpq0dWFkeoXrGRBY_2OnG-FWOLEtpOIFlgMfrU9JOnTgsia94ixdd24hIoA9hBYXfx6QglgAsNEgAMz8ItLj_ICK-INdIrQgfeRFNE3DYaK0EPsWX6AZuFpxyX4i022yFit13vhaCidGQgkVtFuJzx5hig2Rwpj5bLkYhkS6v0DXbsQkLh5kHrA90mR0Ve6gSi6RyRjELElXiC9wHqpZ4Xw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg46002.html>
> My system: x86_64 GNU/Linux
> Freesufer version: freesurfer/6.0.0
> attached the error.log
>
> Best,
> Qi
>
>
>
>
> ___
> Freesurfer mailing 
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[Freesurfer] Tracula group analysis in freesurfer

[Zeng, Qi]

External Email - Use Caution

Hi Experts,

I understand there is surface-based group analysis in Freesurfer, which is
for thickness, curvature, volume and etc. Is there a group analysis for DTI
tracula results? Any links to recommend to conduct the analysis?
Thank you so much!

Best,
Qi
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[Freesurfer] problem running last step longitudinal analysis

[Zeng, Qi]

External Email - Use Caution

Hi Experts,

I am running the last step (-long) for a longitudinal analysis, However,
encountering an error message saying: "error: ERROR: number of asegs and
norm volumes do not match" for all the subjects I run this time. A similar
problem has been reported before as the following link. The answer to the
question is 'Freesufer version too old'. I have been following the exact
same steps two months ago for my last cohort and it was fine. However, this
time all the subjects reporting error messages (attaching error.log).
Re: [Freesurfer] mri_fuse_segmentations error in longitudinal stream
(mail-archive.com)

My system: x86_64 GNU/Linux
Freesufer version: freesurfer/6.0.0
attached the error.log

Best,
Qi


30452536.stdout
Description: Binary data
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[Freesurfer] T1 and DTI nifti data stored after running recon-all and trac-all

[Zeng, Qi]

External Email - Use Caution

Hi,

I run both recon-all and trac-all for each subject. Where are the original
T1 and DTI data stored in the output files?
Thank you so much!

Best,
Qi
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[Freesurfer] DTI scan process steps for single and multiple shells

[Zeng, Qi]

External Email - Use Caution

Hi Freesurfer experts,

Are the steps for processing DTI scan the same for single and multiple
shells? for example, both via -prep, -bedp, -path.
Thank you so much!

Best,
Qi
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[Freesurfer] voxel wise cortical thickness and subcortical volume

[Zeng, Qi]

External Email - Use Caution

Hi,

Is it possible to use Freesurfer to extract global voxel-wise cortical
thickness and subcortical volume?
Thank you so much!

Best,
Qi
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[Freesurfer] longitudinal MRI and DTI registration

[Zeng, Qi]

External Email - Use Caution

Hi,

I was conducting a longitudinal DTI analysis. However, MRI and DTI brain
scans were scheduled at different time frames. Should I be concerned that
for example MRI was taken at 9/1/2006 and nearby DTI was taken on 10/1/2007
or 10/1/2009, which may result in misregistration of DTI given MRI
morphology.

Best,
Qi
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[Freesurfer] outputs from step of trac- all prep

[Zeng, Qi]

External Email - Use Caution

Hi,

Where is the nifti output stored from running trac-all preprocess? Is
it dmri/dwi.nii.gz? Is there an additional step segment this nifti file
into the grey matter and white matter for later tensor-fitting?

Best,
Qi
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Re: [Freesurfer] group level analysis

[Zeng, Qi]

External Email - Use Caution

Now I see. Thank you very much and have a good night!

Best,
Qi

On Mon, Aug 31, 2020 at 11:12 PM Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> Let me put it this way. It's possible that your amygdala is bigger than
> mine without your brain overall being bigger than mine. But if your corpus
> callosum has higher average FA than mine, then your brain overall will have
> higher average FA than mine (assuming we don't have a reverse difference
> somewhere else). Higher average whole-brain FA doesn’t mean that the FA is
> higher *everywhere* in the brain, so it's not a global effect in the way
> that a bigger brain would be a global effect. I hope this makes sense!
> ----------
> *From:* Zeng, Qi 
> *Sent:* Monday, August 31, 2020 10:57 PM
> *To:* Yendiki, Anastasia 
> *Cc:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> Thank you for the clarification! As you said, if I regress out the global
> FA, I could wipe out the regional FA. But what if my question is to find
> out exactly which regional FA differentiate the two groups rather than if
> global FA is different between groups. In that case, should I control the
> global FA when running regional FA between groups?
>
> Best,
> Qi
>
> On Mon, Aug 31, 2020 at 10:41 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or
> surface area measures.
>
> In a situation where a regional FA difference is high enough to also cause
> a whole brain FA difference, regressing out the latter could wipe out the
> former. Not sure why you'd want to do that, unless there's a specific
> question you want to ask that requires it.
>
> Anastasia.
> ------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 10:03 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> Thank you for your reply. So for segmentation.stats, should I divide the
> regional areas by eTIV or treat it as a covariate for a group comparison?
> Is it the same with Total cerebral white matter volume for wmparc.stats.
> For Diffusion measurement, for example, FA, if a subject has lower FA in
> general in the brain, should I adjust the whole brain FA or average FA for
> that matter?
>
> Best,
> Qi
>
> On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Qi - Correcting for overall brain size is important when you are
> comparing measures of length/area/volume. As in, you want to know if a
> region specifically is bigger in population A vs. B, and not just because
> the whole brain is bigger. In that case, use eTIV (estimated total
> intracranial volume) from the freesurfer segmentation stats.
>
> FA is not measuring size of a region, so correcting for brain size is less
> of an issue there. It's a possibility perhaps that for someone with a
> substantially smaller brain there may be more partial voluming affecting
> FA, so it can't hurt to check for an effect before including it in your
> analysis.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 11:44 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi,
>
> When conducting group-level analysis, for example comparing volumetric
> differences or tractography FA across subjects between groups. How we
> correct for the size of the brain when comparing volumetric differences or
> correct for the whole brain FA?
> Thank you so much!
>
> Best,
> Qi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/compliance

Re: [Freesurfer] group level analysis

[Zeng, Qi]

External Email - Use Caution

Hi Anastasia,

Thank you for the clarification! As you said, if I regress out the global
FA, I could wipe out the regional FA. But what if my question is to find
out exactly which regional FA differentiate the two groups rather than if
global FA is different between groups. In that case, should I control the
global FA when running regional FA between groups?

Best,
Qi

On Mon, Aug 31, 2020 at 10:41 PM Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or
> surface area measures.
>
> In a situation where a regional FA difference is high enough to also cause
> a whole brain FA difference, regressing out the latter could wipe out the
> former. Not sure why you'd want to do that, unless there's a specific
> question you want to ask that requires it.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 10:03 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> Thank you for your reply. So for segmentation.stats, should I divide the
> regional areas by eTIV or treat it as a covariate for a group comparison?
> Is it the same with Total cerebral white matter volume for wmparc.stats.
> For Diffusion measurement, for example, FA, if a subject has lower FA in
> general in the brain, should I adjust the whole brain FA or average FA for
> that matter?
>
> Best,
> Qi
>
> On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Qi - Correcting for overall brain size is important when you are
> comparing measures of length/area/volume. As in, you want to know if a
> region specifically is bigger in population A vs. B, and not just because
> the whole brain is bigger. In that case, use eTIV (estimated total
> intracranial volume) from the freesurfer segmentation stats.
>
> FA is not measuring size of a region, so correcting for brain size is less
> of an issue there. It's a possibility perhaps that for someone with a
> substantially smaller brain there may be more partial voluming affecting
> FA, so it can't hurt to check for an effect before including it in your
> analysis.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 11:44 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi,
>
> When conducting group-level analysis, for example comparing volumetric
> differences or tractography FA across subjects between groups. How we
> correct for the size of the brain when comparing volumetric differences or
> correct for the whole brain FA?
> Thank you so much!
>
> Best,
> Qi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>


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Re: [Freesurfer] group level analysis

[Zeng, Qi]

External Email - Use Caution

Hi Anastasia,

Thank you for your reply. So for segmentation.stats, should I divide the
regional areas by eTIV or treat it as a covariate for a group comparison?
Is it the same with Total cerebral white matter volume for wmparc.stats.
For Diffusion measurement, for example, FA, if a subject has lower FA in
general in the brain, should I adjust the whole brain FA or average FA for
that matter?

Best,
Qi

On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia 
wrote:

> Hi Qi - Correcting for overall brain size is important when you are
> comparing measures of length/area/volume. As in, you want to know if a
> region specifically is bigger in population A vs. B, and not just because
> the whole brain is bigger. In that case, use eTIV (estimated total
> intracranial volume) from the freesurfer segmentation stats.
>
> FA is not measuring size of a region, so correcting for brain size is less
> of an issue there. It's a possibility perhaps that for someone with a
> substantially smaller brain there may be more partial voluming affecting
> FA, so it can't hurt to check for an effect before including it in your
> analysis.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 11:44 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi,
>
> When conducting group-level analysis, for example comparing volumetric
> differences or tractography FA across subjects between groups. How we
> correct for the size of the brain when comparing volumetric differences or
> correct for the whole brain FA?
> Thank you so much!
>
> Best,
> Qi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 

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Icahn School of Medicine at Mount Sinai
___
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[Freesurfer] group level analysis

[Zeng, Qi]

External Email - Use Caution

Hi,

When conducting group-level analysis, for example comparing volumetric
differences or tractography FA across subjects between groups. How we
correct for the size of the brain when comparing volumetric differences or
correct for the whole brain FA?
Thank you so much!

Best,
Qi
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[Freesurfer] outlier detection and remove

[Zeng, Qi]

External Email - Use Caution

Hi,

I have a question about how to handle outliers in aparc, aseg and tracula
results? Usually, each subject has one result regarding one measurement and
I detect and remove outliers using barplot. However, for results in
freesurfer, we have multiple outcomes for each region in terms of
measurements of aparc, aseg and tracula. Do we detect outliers for specific
regions or tracts and remove the outliers? Or detect which subjects have
outliers consistently for all the regions, and then we remove the subjects?
Thank you so much !

Best,
Qi

-- 

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Icahn School of Medicine at Mount Sinai
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Re: [Freesurfer] T1 stats output name confused

[Zeng, Qi]

External Email - Use Caution

Hi Douglas,

So basically, aparc+aseg.stats are generated from aparc+aseg.mgz, which
segment T1-weighted image into gray matter, white matter, ventricles,
non-ventricular cerebrospinal fluid and lesion. Is that correct?
Thank you !

Best,
Qi

On Mon, Jun 15, 2020 at 10:28 AM Douglas N. Greve 
wrote:

> I'm not sure what you mean. Are you looking for a single file that
> contains all the info? If so, the answer is no, we do not output such a file
>
> On 6/13/2020 5:10 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> So from what I understand, there is no straightforward file containing
> white matter and grey matter stats. Is that correct?
>
> Best,
> Qi
>
> On Fri, Jun 12, 2020 at 5:45 PM Douglas N. Greve 
> wrote:
>
>> seg is usually a volume-based segmentation (like the aseg)
>> parc is usually a surface-based segmentation (like lh.aparc.annot)
>> unfortunately, I misnamed "wmparc". It is a volume-based segmentation
>> that incorporates surface-based information
>>
>> On 6/12/2020 3:12 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> Hi All,
>>
>> I am a little confused with the stats output. So seg/aparc are cortical
>> white /grey matter and wmparc are subcortical white matter. Is that correct?
>>
>> Best,
>> Qi
>>
>>
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 

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Icahn School of Medicine at Mount Sinai
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Freesurfer mailing list
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Re: [Freesurfer] T1 stats output name confused

[Zeng, Qi]

External Email - Use Caution

So from what I understand, there is no straightforward file containing
white matter and grey matter stats. Is that correct?

Best,
Qi

On Fri, Jun 12, 2020 at 5:45 PM Douglas N. Greve 
wrote:

> seg is usually a volume-based segmentation (like the aseg)
> parc is usually a surface-based segmentation (like lh.aparc.annot)
> unfortunately, I misnamed "wmparc". It is a volume-based segmentation that
> incorporates surface-based information
>
> On 6/12/2020 3:12 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi All,
>
> I am a little confused with the stats output. So seg/aparc are cortical
> white /grey matter and wmparc are subcortical white matter. Is that correct?
>
> Best,
> Qi
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] T1 stats output name confused

[Zeng, Qi]

External Email - Use Caution

Hi All,

I am a little confused with the stats output. So seg/aparc are cortical
white /grey matter and wmparc are subcortical white matter. Is that correct?

Best,
Qi
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Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

[Zeng, Qi]

External Email - Use Caution

Hi Juan,

If I want to seed T1 hippocampus.mgz to fill the ProbtrackX. How should I
do that?
Is it something like below:
mris_convert lh.white lh.white.gii
mri_convert lh.hippocampus.mgz lh.hippocampus.nii.gz
and then
label2surf -s lh.white.gii -o lh.hippocampus.nii.gz -l hippocampus.txt

Thank you so much !

Best,
Qi


On Fri, Jun 5, 2020 at 4:13 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> Removing the -U ;-)
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, June 5, 2020 at 16:02
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Get hippocampus segmention from
> [lr]h.hippoAmygLabels-T1.v21.mgz
>
>
>
> *External Email - Use Caution*
>
> Thanks. I was wondering If there is another way around to get the amygdala
> mgz.
>
>
>
> Best,
>
> Qi
>
>
>
> On Fri, Jun 5, 2020 at 2:44 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> Yes    the amydala labels are in the 7000 range and the hippocampal in
> the 200s. Feel free to use eg 4129 next time!
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, June 5, 2020 at 14:42
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Get hippocampus segmention from
> [lr]h.hippoAmygLabels-T1.v21.mgz
>
>
>
> *External Email - Use Caution*
>
> Thanks, it works. Does the code mean that it only allows labels under 300
> to pass through?
>
>
>
> Best,
>
> Qi
>
>
>
> On Fri, Jun 5, 2020 at 12:37 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> Dear Qi,
>
> You can try:
>
> mri_threshold -U  [lr]h.hippoAmygLabels-T1.v21.mgz 300
> [lr]h.hippoLabelsNoAmyg-T1.v21.mgz
>
>
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, June 5, 2020 at 11:54
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Get hippocampus segmention from
> [lr]h.hippoAmygLabels-T1.v21.mgz
>
>
>
> *External Email - Use Caution*
>
> Hi,
>
>
>
> I conducted longitudinal segmentation of both hippocampus and amygdala
> from running segmentHA_T1_long.sh. But is it possible for me to segment
> only the hippocampus region "mgz" from the stored
> [lr]h.hippoAmygLabels-T1.long.v21.mgz ?
>
>
>
> Best,
>
> Qi
>
>
> --
>
>
>
> Ph.D. candidate
>
> Icahn School of Medicine at Mount Sinai
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
>
>
>
> Ph.D. candidate
>
> Icahn School of Medicine at Mount Sinai
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
>
>
>
> Ph.D. candidate
>
> Icahn School of Medicine at Mount Sinai
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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Icahn School of Medicine at Mount Sinai
___
Freesurfer mailing list
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Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

[Zeng, Qi]

External Email - Use Caution

Thanks. I was wondering If there is another way around to get the amygdala
mgz.

Best,
Qi

On Fri, Jun 5, 2020 at 2:44 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> Yes    the amydala labels are in the 7000 range and the hippocampal in
> the 200s. Feel free to use eg 4129 next time!
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, June 5, 2020 at 14:42
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Get hippocampus segmention from
> [lr]h.hippoAmygLabels-T1.v21.mgz
>
>
>
> *External Email - Use Caution*
>
> Thanks, it works. Does the code mean that it only allows labels under 300
> to pass through?
>
>
>
> Best,
>
> Qi
>
>
>
> On Fri, Jun 5, 2020 at 12:37 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> Dear Qi,
>
> You can try:
>
> mri_threshold -U  [lr]h.hippoAmygLabels-T1.v21.mgz 300
> [lr]h.hippoLabelsNoAmyg-T1.v21.mgz
>
>
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, June 5, 2020 at 11:54
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Get hippocampus segmention from
> [lr]h.hippoAmygLabels-T1.v21.mgz
>
>
>
> *External Email - Use Caution*
>
> Hi,
>
>
>
> I conducted longitudinal segmentation of both hippocampus and amygdala
> from running segmentHA_T1_long.sh. But is it possible for me to segment
> only the hippocampus region "mgz" from the stored
> [lr]h.hippoAmygLabels-T1.long.v21.mgz ?
>
>
>
> Best,
>
> Qi
>
>
> --
>
>
>
> Ph.D. candidate
>
> Icahn School of Medicine at Mount Sinai
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
>
>
>
> Ph.D. candidate
>
> Icahn School of Medicine at Mount Sinai
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 

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Icahn School of Medicine at Mount Sinai
___
Freesurfer mailing list
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Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

[Zeng, Qi]

External Email - Use Caution

Thanks, it works. Does the code mean that it only allows labels under 300
to pass through?

Best,
Qi

On Fri, Jun 5, 2020 at 12:37 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> Dear Qi,
>
> You can try:
>
> mri_threshold -U  [lr]h.hippoAmygLabels-T1.v21.mgz 300
> [lr]h.hippoLabelsNoAmyg-T1.v21.mgz
>
>
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, June 5, 2020 at 11:54
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Get hippocampus segmention from
> [lr]h.hippoAmygLabels-T1.v21.mgz
>
>
>
> *External Email - Use Caution*
>
> Hi,
>
>
>
> I conducted longitudinal segmentation of both hippocampus and amygdala
> from running segmentHA_T1_long.sh. But is it possible for me to segment
> only the hippocampus region "mgz" from the stored
> [lr]h.hippoAmygLabels-T1.long.v21.mgz ?
>
>
>
> Best,
>
> Qi
>
>
> --
>
>
>
> Ph.D. candidate
>
> Icahn School of Medicine at Mount Sinai
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

[Zeng, Qi]

External Email - Use Caution

Hi,

I conducted longitudinal segmentation of both hippocampus and amygdala from
running segmentHA_T1_long.sh. But is it possible for me to segment only the
hippocampus region "mgz" from the stored
[lr]h.hippoAmygLabels-T1.long.v21.mgz ?

Best,
Qi

-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] longitudinal trac -prep missing outputs

[Zeng, Qi]

External Email - Use Caution

Hi,

I was running longitudinal trac-all. After the 3rd step -path was finished,
I found that multiple pathways were missing (e.g. fminor). I traced back,
realizing outputs from its first step trac-prep were missing corresponding
pathways in SUBJ_base/dlabel/mni/fminor. However, the scripts of
SUBJ_base_long_ses-1 and ses-2 both claimed "trac-preproc finished without
error". I double checked the bval, bvec and DTI and increased the memory
limit, the same problem still exists. So I was wondering how to fix it.
Attached the compressed log file of SUBJ_base of trac -prep (too big).


Best,
Qi

-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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Re: [Freesurfer] tracula stats summary

[Zeng, Qi]

External Email - Use Caution

Already Solved. Thank you so much!

Best,
Qi

On Fri, May 8, 2020 at 10:46 AM Yendiki, Anastasia 
wrote:

> If you're not happy with the output of tractstats2table and want something
> custom, you can just do a search in the stats files. They're simple text
> files. You can see how these files are named and what their contents look
> like here:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics#Anisotropyanddiffusivityaveragedoveranentirepathway
>
> You'd have to search for the lines that contain subjectname, pathwayname,
> and the name of the diffusion measure that you want.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Friday, May 8, 2020 9:58 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] tracula stats summary
>
>
> External Email - Use Caution
>
> Hi,
>
> Is it possible to collect all 18 tracts stats into a single file?
> Has tried:
> "tractstats2table --load-pathstats-from-file paths.txt --overall
> --tablefile tractAll.txt"
> Path.txt contains all the subjects' 18 paths' full path directory
> Error message:
> "all stats files need to have the same pathwayname. try verbose option
> These are the pathwaynames found: ['fmajor', 'fminor', 'lh.atr', 'lh.cab',
> 'lh.ccg', 'lh.cst', 'lh.ilf', 'lh.slfp', 'lh.slft', 'lh.unc', 'rh.atr',
> 'rh.cab', 'rh.ccg', 'rh.cst', 'rh.ilf', 'rh.slfp', 'rh.slft', 'rh.unc']"
>
> Best,
> Qi
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
___
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[Freesurfer] tracula stats summary

[Zeng, Qi]

External Email - Use Caution

Hi,

Is it possible to collect all 18 tracts stats into a single file?
Has tried:
"tractstats2table --load-pathstats-from-file paths.txt --overall
--tablefile tractAll.txt"
Path.txt contains all the subjects' 18 paths' full path directory
Error message:
"all stats files need to have the same pathwayname. try verbose option
These are the pathwaynames found: ['fmajor', 'fminor', 'lh.atr', 'lh.cab',
'lh.ccg', 'lh.cst', 'lh.ilf', 'lh.slfp', 'lh.slft', 'lh.unc', 'rh.atr',
'rh.cab', 'rh.ccg', 'rh.cst', 'rh.ilf', 'rh.slfp', 'rh.slft', 'rh.unc']"

Best,
Qi

-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

[Zeng, Qi]

External Email - Use Caution

Hi Eugenio,

Another information: though script exited with errors, all the left
hemispheres generated hippoSFVolums and amydNucVolumes as outputs. Missing
right hemispheres for all.

Best,
Qi

On Mon, May 4, 2020 at 12:44 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> Dear Qi,
>
> I’m really sorry you’re running into all these problem.
>
> We’ll look into it and get back to you asap
>
> Cheers,
>
> /Eugenio
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, May 4, 2020 at 12:37
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio,
>
>
>
> I installed freesurfer/7.0.0 and ran longitudinal hippocampal & amygdala
> subfields again. Error message indicates:
>
> "Error in SegmentSubfieldsT1Longitudinal (line 1795)". I have attached the
> log file.
>
> Can you help figure this out?
>
>
>
> Thank you so much !
>
> Best,
>
> Qi
>
>
>
>
>
>
>
>
>
>
>
> On Fri, May 1, 2020 at 1:35 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> That’s easy ;-)
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/License
>
>
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, May 1, 2020 at 12:28
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio,
>
>
>
> I installed the FS7.0.0 and matlab_runtime/R2014b and ran a longitudinal
> hippocampal subfield again. Get following errors:
>
> "ERROR: FreeSurfer license file
> /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/.license not
> found"
>
> and
>
> same error "Error in kvlReadCroppedImage (line 11)
>
> Error in SegmentSubfieldsT1Longitudinal (line 403)"
>
> Where do I find the Freesurfer license? Here attached the log file.
>
>
>
> Thank you so much!
>
> Best,
>
> Qi
>
>
>
>
>
> On Thu, Apr 30, 2020 at 1:38 PM Zeng, Qi  wrote:
>
> Thank you so much. I will upgrade the dev and run it again, fingers
> crossed.
>
>
>
> Best,
>
> Qi
>
>
>
>
>
>
>
> On Thu, Apr 30, 2020 at 1:25 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> Ah! I think you were unlucky enough to download the dev version literally
> days before we fixed these issues ;-)
>
> If you upgrade to the latest dev, it should be fixed! Or, wait a bit until
> FS7 comes out, there’s rumors that it may be pretty soon.
>
> Cheers,
>
> /E
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, April 30, 2020 at 12:48
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio:
>
> recon -all --version
>
> freesurfer-linux-centos6_x86_64-dev-20180509-5a99f28
>
> operating system: Linux
>
>
>
> Best,
>
> Qi
>
>
>
>
>
>
>
> On Thu, Apr 30, 2020 at 12:06 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> This was very helpful, thanks. Can you please send me the output of the
> following command?
>
> recon-all --version
>
> as well as your operating system?
>
> Cheers,
>
> /Eugenio
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi&qu

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

[Zeng, Qi]

External Email - Use Caution

Thank you so much !

Best,
Qi

On Mon, May 4, 2020 at 12:44 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> Dear Qi,
>
> I’m really sorry you’re running into all these problem.
>
> We’ll look into it and get back to you asap
>
> Cheers,
>
> /Eugenio
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, May 4, 2020 at 12:37
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio,
>
>
>
> I installed freesurfer/7.0.0 and ran longitudinal hippocampal & amygdala
> subfields again. Error message indicates:
>
> "Error in SegmentSubfieldsT1Longitudinal (line 1795)". I have attached the
> log file.
>
> Can you help figure this out?
>
>
>
> Thank you so much !
>
> Best,
>
> Qi
>
>
>
>
>
>
>
>
>
>
>
> On Fri, May 1, 2020 at 1:35 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> That’s easy ;-)
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/License
>
>
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, May 1, 2020 at 12:28
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio,
>
>
>
> I installed the FS7.0.0 and matlab_runtime/R2014b and ran a longitudinal
> hippocampal subfield again. Get following errors:
>
> "ERROR: FreeSurfer license file
> /hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/.license not
> found"
>
> and
>
> same error "Error in kvlReadCroppedImage (line 11)
>
> Error in SegmentSubfieldsT1Longitudinal (line 403)"
>
> Where do I find the Freesurfer license? Here attached the log file.
>
>
>
> Thank you so much!
>
> Best,
>
> Qi
>
>
>
>
>
> On Thu, Apr 30, 2020 at 1:38 PM Zeng, Qi  wrote:
>
> Thank you so much. I will upgrade the dev and run it again, fingers
> crossed.
>
>
>
> Best,
>
> Qi
>
>
>
>
>
>
>
> On Thu, Apr 30, 2020 at 1:25 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> Ah! I think you were unlucky enough to download the dev version literally
> days before we fixed these issues ;-)
>
> If you upgrade to the latest dev, it should be fixed! Or, wait a bit until
> FS7 comes out, there’s rumors that it may be pretty soon.
>
> Cheers,
>
> /E
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, April 30, 2020 at 12:48
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio:
>
> recon -all --version
>
> freesurfer-linux-centos6_x86_64-dev-20180509-5a99f28
>
> operating system: Linux
>
>
>
> Best,
>
> Qi
>
>
>
>
>
>
>
> On Thu, Apr 30, 2020 at 12:06 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> This was very helpful, thanks. Can you please send me the output of the
> following command?
>
> recon-all --version
>
> as well as your operating system?
>
> Cheers,
>
> /Eugenio
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, April 30, 2020 at 09:55
> *To: *Freesurfer support list 
> *S

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

[Zeng, Qi]

External Email - Use Caution

Hi Eugenio,

I installed the FS7.0.0 and matlab_runtime/R2014b and ran a longitudinal
hippocampal subfield again. Get following errors:
"ERROR: FreeSurfer license file
/hpc/packages/minerva-centos7/freesurfer/7.0.0/freesurfer/.license not
found"
and
same error "Error in kvlReadCroppedImage (line 11)
Error in SegmentSubfieldsT1Longitudinal (line 403)"
Where do I find the Freesurfer license? Here attached the log file.

Thank you so much!
Best,
Qi


On Thu, Apr 30, 2020 at 1:38 PM Zeng, Qi  wrote:

> Thank you so much. I will upgrade the dev and run it again, fingers
> crossed.
>
> Best,
> Qi
>
>
>
> On Thu, Apr 30, 2020 at 1:25 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
>> Ah! I think you were unlucky enough to download the dev version
>> literally days before we fixed these issues ;-)
>>
>> If you upgrade to the latest dev, it should be fixed! Or, wait a bit
>> until FS7 comes out, there’s rumors that it may be pretty soon.
>>
>> Cheers,
>>
>> /E
>>
>>
>>
>>
>>
>> Juan Eugenio Iglesias
>>
>> Senior research fellow
>>
>> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>>
>> http://www.jeiglesias.com
>>
>>
>>
>>
>>
>>
>>
>> *From: * on behalf of "Zeng, Qi"
>> 
>> *Reply-To: *Freesurfer support list 
>> *Date: *Thursday, April 30, 2020 at 12:48
>> *To: *Freesurfer support list 
>> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
>> existed with errors
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Eugenio:
>>
>> recon -all --version
>>
>> freesurfer-linux-centos6_x86_64-dev-20180509-5a99f28
>>
>> operating system: Linux
>>
>>
>>
>> Best,
>>
>> Qi
>>
>>
>>
>>
>>
>>
>>
>> On Thu, Apr 30, 2020 at 12:06 PM Iglesias Gonzalez, Juan E. <
>> jiglesiasgonza...@mgh.harvard.edu> wrote:
>>
>> This was very helpful, thanks. Can you please send me the output of the
>> following command?
>>
>> recon-all --version
>>
>> as well as your operating system?
>>
>> Cheers,
>>
>> /Eugenio
>>
>>
>>
>> Juan Eugenio Iglesias
>>
>> Senior research fellow
>>
>> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>>
>> http://www.jeiglesias.com
>>
>>
>>
>>
>>
>>
>>
>> *From: * on behalf of "Zeng, Qi"
>> 
>> *Reply-To: *Freesurfer support list 
>> *Date: *Thursday, April 30, 2020 at 09:55
>> *To: *Freesurfer support list 
>> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
>> existed with errors
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Eugenio,
>>
>>
>>
>> Sorry, this one is from another individual from the control group. Here
>> attached the error script I described. Sorry for the confusion.
>>
>>
>>
>> Best,
>>
>> Qi
>>
>>
>>
>> On Wed, Apr 29, 2020 at 5:47 PM Iglesias Gonzalez, Juan E. <
>> jiglesiasgonza...@mgh.harvard.edu> wrote:
>>
>> Wait but this isn’t the error your first described…?
>>
>>
>>
>>
>>
>> Juan Eugenio Iglesias
>>
>> Senior research fellow
>>
>> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>>
>> http://www.jeiglesias.com
>>
>>
>>
>>
>>
>>
>>
>> *From: * on behalf of "Zeng, Qi"
>> 
>> *Reply-To: *Freesurfer support list 
>> *Date: *Wednesday, April 29, 2020 at 17:28
>> *To: *Freesurfer support list 
>> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
>> existed with errors
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Eugenio,
>>
>>
>>
>> Thank you so much for the prompt reply !
>>
>> Here attached the log file.
>>
>> The files generated:
>>
>> SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left
>>
>> SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1
>>
>>
>>
>> Best,
>>
>> Qi
>>
>>
>>
>>
>>
>> On Wed, Apr 29, 2020 at 5:22 PM Zeng, Qi  wrote:
>>
>> Hi Eugenio,
>>
>>
>>
>> Thank you so much for the prompt reply !
>>
>> Here attached the output error and

[Freesurfer] longitudinal trac-all -path exited with error

[Zeng, Qi]

External Email - Use Caution

Hi,

My trac-all -path exited with error after trying to load BEDPOST parameter
samples from SUBJ.long.SUBJ_base/dmri.bedpostX. So is there something wrong
with my bedpostX from trac-all -bedp? Should I run bedpostX separately
again without trac-all. Though my last step '-bedp' didn't prompt 'finished
without error' log message as preproc did, expected files were created.
BTW, which log script should I look into? the one follows
SUBJ_base/script or SUBJ_ses-1.long.SUBJ_base/script? Here attached the
trac-all -path log.

Thank you so much!
Best,
Qi

-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai


9163803.stdout
Description: Binary data
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Re: [Freesurfer] trac-all -bedp error

[Zeng, Qi]

External Email - Use Caution

Anastasia, thank you so much !

On Thu, Apr 30, 2020 at 8:03 PM Yendiki, Anastasia 
wrote:

> Yes, this is fine.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Thursday, April 30, 2020 2:22 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] trac-all -bedp error
>
>
> External Email - Use Caution
>
> Hi,
>
> I run trac-all, the log file has the following endings.
> "Queuing post processing stage"
> or
> "Queuing post processing stage
> 59 slices processed
> All slices processed
> /hpc/packages/minerva-common/freesurfer/6.0.0/freesurfer/bin/bedpostx_mgh:
> line 345: kill: (100952) - No such process".
>
> However, all outputs described in FSL BedpostX are generated
> dmri/FA, MD, V1, V2, V3
> dmri.bedpostX/merged,mean,dyads, nodif_brain_mask
>
> Should I consider them as completed and move forward with -path?
>
> Best,
> Qi
>
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] longitudinal dmrirc script error with the baselist

[Zeng, Qi]

External Email - Use Caution

Hi Anastasia,

I think there are some misunderstandings here. I have created one
configuration file for each subject and it works processing longitudinal
data. And since all my subjects are stored following /subjects/ in one
directory, I assumed adding individual 'SUBJ1/' to the file would work.
Here attached my individual and multiple subjects' configuration file. Can
you help take a look? From what you say, I have some suspicion that my
individual configuration could also have some problem.
Thank you so much !

Best,
Qi




On Thu, Apr 30, 2020 at 4:41 PM Yendiki, Anastasia 
wrote:

> You cannot have multiple SUBJECTS_DIR's. It is supposed to be the base
> directory under which all subjects' dirs are saved. You could have a
> different configuration file for each subject if you want each of them to
> have a different SUBJECTS_DIR, but this hack won't work for longitudinal
> analyses as all the time points from the same subject have to be defined in
> the same config file. If you must have subjects saved in different
> locations, you can create a "mock" SUBJECTS_DIR and in it create symlinks
> to the dirs of every individual subject (this includes both *.long.* and
> base dirs).
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Thursday, April 30, 2020 3:40 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] longitudinal dmrirc script error with the baselist
>
>
> External Email - Use Caution
>
> Hi,
>
> I have my trac-all up and running with no error with individual subjects
> when I set the subject directory to individual subjects.
> as follow:
> set SUBJECTS_DIR=/*/subjects/SUBJ1
> set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2)
> set baselist = (SUBJ1_base SUBJ1_base)
>
> However, when I put subjects together and set the directory to multiple
> subjects as follow:
> set SUBJECTS_DIR=/*/subjects
> set subjlist = (SUBJ1/SUBJ1_ses-1 \
>   SUBJ1/SUBJ1_ses-2 \
>   SUBJ2/SUBJ2_ses-1 \
>   SUBJ2/SUBJ2_ses-2 \
>   etc. )
> set baselist = (SUBJ1/SUBJ1_base \
>SUBJ1/SUBJ1_base \
>SUBJ2/SUBJ2_base \
>SUBJ2/SUBJ2_base \
>etc.)
>
> It has a problem finding the baselist file:
> "cannot find /*/subjects/SUBJ1/SUBJ1_ses-1.long.SUBJ1/SUBJ1_base". Should
> I copy SUJB1_base under the SUBJ1.long.SUBJ1 and run it again? Why is it
> not happening with the subject individual?
>
> Best,
> Qi
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# set 
SUBJECTS_DIR=/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects

# output directory (same as SUBJECTS_DIR)
set dtroot = 
/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects

# Subject IDs (one per time point per subject)
set subjlist = (003_S_4288/003_S_4288_ses-1 003_S_4288/003_S_4288_ses-2 
029_S_4385/029_S_4385_ses-1 029_S_4385/029_S_4385_ses-2 
029_S_4652/029_S_4652_ses-1 029_S_4652/029_S_4652_ses-2 
029_S_5166/029_S_5166_ses-1 029_S_5166/029_S_5166_ses-2 
098_S_0896/098_S_0896_ses-1 098_S_0896/098_S_0896_ses-2 
098_S_4275/098_S_4275_ses-1 098_S_4275/098_S_4275_ses-2 
098_S_4506/098_S_4506_ses-1 098_S_4506/098_S_4506_ses-2 
126_S_5214/126_S_5214_ses-1 126_S_5214/126_S_5214_ses-2)

# Longitudinal base template subject IDs (one for each time point above)
set baselist = (003_S_4288/003_S_4288_base 003_S_4288/003_S_4288_base 
029_S_4385/029_S_4385_base 029_S_4385/029_S_4385_base 
029_S_4652/029_S_4652_base 029_S_4652/029_S_4652_base 
029_S_5166/029_S_5166_base 029_S_5166/029_S_5166_base 
098_S_0896/098_S_0896_base 098_S_0896/098_S_0896_base 
098_S_4275/098_S_4275_base 098_S_4275/098_S_4275_base 
098_S_4506/098_S_4506_base 098_S_4506/098_S_4506_base 
126_S_5214/126_S_5214_base 126_S_5214/126_S_5214_base)

# Default: Run analysis on all time points and subjects
set runlist = (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16)

# Input diffusion DICOMs (file names relative to dcmroot)
set dcmroot = 
/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects
set dcmlist = (003_S_4288/DTI/DTI_ses-1/003_S_4288.nii.gz 
003_S_4288/DTI/DTI_ses-2/003_S_4288.nii.gz 
029_S_4385/DTI/DTI_ses-1/029_S_4

[Freesurfer] longitudinal dmrirc script error with the baselist

[Zeng, Qi]

External Email - Use Caution

Hi,

I have my trac-all up and running with no error with individual subjects
when I set the subject directory to individual subjects.
as follow:
set SUBJECTS_DIR=/*/subjects/SUBJ1
set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2)
set baselist = (SUBJ1_base SUBJ1_base)

However, when I put subjects together and set the directory to multiple
subjects as follow:
set SUBJECTS_DIR=/*/subjects
set subjlist = (SUBJ1/SUBJ1_ses-1 \
  SUBJ1/SUBJ1_ses-2 \
  SUBJ2/SUBJ2_ses-1 \
  SUBJ2/SUBJ2_ses-2 \
  etc. )
set baselist = (SUBJ1/SUBJ1_base \
   SUBJ1/SUBJ1_base \
   SUBJ2/SUBJ2_base \
   SUBJ2/SUBJ2_base \
   etc.)

It has a problem finding the baselist file:
"cannot find /*/subjects/SUBJ1/SUBJ1_ses-1.long.SUBJ1/SUBJ1_base". Should I
copy SUJB1_base under the SUBJ1.long.SUBJ1 and run it again? Why is it not
happening with the subject individual?

Best,
Qi

-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
___
Freesurfer mailing list
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[Freesurfer] trac-all -bedp error

[Zeng, Qi]

External Email - Use Caution

Hi,

I run trac-all, the log file has the following endings.
"Queuing post processing stage"
or
"Queuing post processing stage
59 slices processed
All slices processed
/hpc/packages/minerva-common/freesurfer/6.0.0/freesurfer/bin/bedpostx_mgh:
line 345: kill: (100952) - No such process".

However, all outputs described in FSL BedpostX are generated
dmri/FA, MD, V1, V2, V3
dmri.bedpostX/merged,mean,dyads, nodif_brain_mask

Should I consider them as completed and move forward with -path?

Best,
Qi


-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
___
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Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

[Zeng, Qi]

External Email - Use Caution

Thank you so much. I will upgrade the dev and run it again, fingers
crossed.

Best,
Qi



On Thu, Apr 30, 2020 at 1:25 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> Ah! I think you were unlucky enough to download the dev version literally
> days before we fixed these issues ;-)
>
> If you upgrade to the latest dev, it should be fixed! Or, wait a bit until
> FS7 comes out, there’s rumors that it may be pretty soon.
>
> Cheers,
>
> /E
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, April 30, 2020 at 12:48
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio:
>
> recon -all --version
>
> freesurfer-linux-centos6_x86_64-dev-20180509-5a99f28
>
> operating system: Linux
>
>
>
> Best,
>
> Qi
>
>
>
>
>
>
>
> On Thu, Apr 30, 2020 at 12:06 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> This was very helpful, thanks. Can you please send me the output of the
> following command?
>
> recon-all --version
>
> as well as your operating system?
>
> Cheers,
>
> /Eugenio
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, April 30, 2020 at 09:55
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio,
>
>
>
> Sorry, this one is from another individual from the control group. Here
> attached the error script I described. Sorry for the confusion.
>
>
>
> Best,
>
> Qi
>
>
>
> On Wed, Apr 29, 2020 at 5:47 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> Wait but this isn’t the error your first described…?
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, April 29, 2020 at 17:28
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio,
>
>
>
> Thank you so much for the prompt reply !
>
> Here attached the log file.
>
> The files generated:
>
> SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left
>
> SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1
>
>
>
> Best,
>
> Qi
>
>
>
>
>
> On Wed, Apr 29, 2020 at 5:22 PM Zeng, Qi  wrote:
>
> Hi Eugenio,
>
>
>
> Thank you so much for the prompt reply !
>
> Here attached the output error and log file.
>
> The files generated:
>
> SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left
>
> SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1
>
>
>
> Best,
>
> Qi
>
>
>
> On Wed, Apr 29, 2020 at 3:23 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> Dear Qi,
>
> The correct syntax is that of your First try, but I’m very surprised you
> got that error, as we fixed this  a while ago… Can you please send me the
> complete output?
>
> Cheers,
>
> /Eugenio
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, April 29, 2020 at 04:44
> *To: *"freesurfer@nmr.mgh.harvard.edu" 
> *Subject: *[Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi,
>
> I am trying to use 

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

[Zeng, Qi]

External Email - Use Caution

Hi Eugenio:
recon -all --version
freesurfer-linux-centos6_x86_64-dev-20180509-5a99f28
operating system: Linux

Best,
Qi



On Thu, Apr 30, 2020 at 12:06 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> This was very helpful, thanks. Can you please send me the output of the
> following command?
>
> recon-all --version
>
> as well as your operating system?
>
> Cheers,
>
> /Eugenio
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, April 30, 2020 at 09:55
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi Eugenio,
>
>
>
> Sorry, this one is from another individual from the control group. Here
> attached the error script I described. Sorry for the confusion.
>
>
>
> Best,
>
> Qi
>
>
>
> On Wed, Apr 29, 2020 at 5:47 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> Wait but this isn’t the error your first described…?
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, April 29, 2020 at 17:28
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution    *
>
> Hi Eugenio,
>
>
>
> Thank you so much for the prompt reply !
>
> Here attached the log file.
>
> The files generated:
>
> SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left
>
> SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1
>
>
>
> Best,
>
> Qi
>
>
>
>
>
> On Wed, Apr 29, 2020 at 5:22 PM Zeng, Qi  wrote:
>
> Hi Eugenio,
>
>
>
> Thank you so much for the prompt reply !
>
> Here attached the output error and log file.
>
> The files generated:
>
> SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left
>
> SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1
>
>
>
> Best,
>
> Qi
>
>
>
> On Wed, Apr 29, 2020 at 3:23 PM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
> Dear Qi,
>
> The correct syntax is that of your First try, but I’m very surprised you
> got that error, as we fixed this  a while ago… Can you please send me the
> complete output?
>
> Cheers,
>
> /Eugenio
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, April 29, 2020 at 04:44
> *To: *"freesurfer@nmr.mgh.harvard.edu" 
> *Subject: *[Freesurfer] Longitudinal Hippocampal Subfields Module,
> existed with errors
>
>
>
> *External Email - Use Caution*
>
> Hi,
>
> I am trying to use the longitudinal pipeline of the “hippocampal subfields
> and nuclei of amygdala”. Keep getting error messages when running it
> longitudinal but with no error message running it cross-sectional. I want
> to know if there is any way to fix the error and to run a longitudinal
> pipeline successfully.
>
> I am using Freesurfer/dev and matlab_runtime/2014b.
>
> I got two timepoints for each subject and finished recon-all longitudinal
> with no errors.
>
> 1) First Try
>
> segmentHA_T1_long.sh SUBJ_base
>
> >> run for about 15 mins and exited with error message:
>
> “Error using kvlGEMSMatlab
>
>
> /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMeshDeformationOptimizer.cxx:327:
>
> itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2ac1fead7740): search
> direction is not a descent direction!
>
> Error in kvlStepOptimizer (line 11)
>
> Error in SegmentSubfieldsT1Longitudinal”
>
> >> no mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21
> generated.
>
>
>
> 2) Second Try
>
> segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_base
>
> 

[Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

[Zeng, Qi]

External Email - Use Caution

Hi,

I am trying to use the longitudinal pipeline of the “hippocampal subfields
and nuclei of amygdala”. Keep getting error messages when running it
longitudinal but with no error message running it cross-sectional. I want
to know if there is any way to fix the error and to run a longitudinal
pipeline successfully.

I am using Freesurfer/dev and matlab_runtime/2014b.

I got two timepoints for each subject and finished recon-all longitudinal
with no errors.

1) First Try

segmentHA_T1_long.sh SUBJ_base

>> run for about 15 mins and exited with error message:

“Error using kvlGEMSMatlab

/autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMeshDeformationOptimizer.cxx:327:

itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2ac1fead7740): search
direction is not a descent direction!

Error in kvlStepOptimizer (line 11)

Error in SegmentSubfieldsT1Longitudinal”

>> no mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21
generated.


2) Second Try

segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_base

segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_base

>> run for about 16 mins, most successful but a few with errors:

“Error in segmentSubjectT1_autoEstimateAlveusML (line 1539)”

Or

>>

“Open file failed because file
'/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m'
has invalid content. Details: 'file is closed.failbit is set.'

The file

 
"/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m"

cannot be executed.

Error in segmentSubjectT1_autoEstimateAlveusML (line 538)”



>> successful done subject or hemisphere generated
mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21.



3) Third Try cross-sectional

segmentHA_T1.sh SUBJ1_timepoint1

segmentHA_T1.sh SUBJ1_timepoint2

>> run for about 15 mins, all successful with no errors:

>> all subjects have mri/lh.amygNucVolumes-T1.v21 and
mri/lh.hippoSfVolumes-T1.v21 generated.


Manual inspection with freeview, it seems fine with all successful
longitudinal and cross sectional subfield segmentation outputs mgz.


I wonder if I can fix first try and second try errors so that longitudinal
output can be generated.



Thank you for your help!

Best,

Qi


-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
___
Freesurfer mailing list
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[Freesurfer] trac-all problem

[Zeng, Qi]

Hi,

I am running dti data with trac-all. I followed the command:

trac-all -prep -c /Studies/*/DTI/dmrirc_subject

but it exited with error "*Note: indexing (in both time and space)
starts with 0 not 1! Inputting -1 for a size will set it to the full
image extent for that dimension." *

Before. there is another post about similar problem

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027802.html

Dr. Yendiki suggested it could be because missing defined B0 in the
dmrirc, but new version wouldn't need this (5.3, a new version?). If
so, where can I obtain the B0 data? Can I compute from DICOM like
nifti and bval, bvec?

Best,

Qi
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[Freesurfer] patient case study at two time points

[Zeng, Qi]

Hi All,

I was running freesurfer for a patient case of two time points. Will you
suggest to run it as a group, such as one time point as a template and
followed by longitudinal study, discussing atrophy or run these two time
points separately as two individual, running everything such recon-all,
dt-recon twice and comparing the result, such as thickness, volume and FA?
BTW, I post a question about FA display before: will anything lead to a
rectangular FA display, with extra diffusion out of the brain skull (no
errors during recon and dt …)?

Best,
Qi
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