[Freesurfer] modify intensity normalization pipeline

2024-01-05 Thread Carlos Alcocer 
External Email - Use Caution

Hello,

Is there a way to modify intensity normalization pipeline in recon-all
script? The temporal lobe is being very poorly segmented because white
matter is being segmented as gray matter and therefore gray matter does not
reach outer boundary of pial surface.

Thank you,

Carlos
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[Freesurfer] poor inferior cerebellum segmentation

2024-01-05 Thread Carlos Alcocer 
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Hello,

Inferior portion of cerebellum are not segmented well. It is included in
skullstrip and I tried adding control points in cerebellar WM but this did
not help. I am not interested in cerebellum but I do need eTIV. Will this
poor cerebellar segmentation affect eTIV calculation?

Thank you,

Carlos
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[Freesurfer] recon-all error

2023-11-16 Thread Carlos Alcocer 
External Email - Use Caution

Hi,

For some of my subjects I get the following error at the beginning of
recon-all:

 mri_convert /path/to/inputt1.nii  /path/to/mri/orig/001.mgz

mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz
reading from /path/to/anat_t1.nii...
NaN found at voxel (0, 0, 244, 0)
error: No such file or directory
error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii...

However, recon-all will keep running and then later finish without error.
What exactly is going on? This is only happens on some subjects.

Thank you,

Carlos
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Re: [Freesurfer] Calculate cortical thickness of a volumetric ROI

2023-07-14 Thread Carlos Alcocer 
External Email - Use Caution

Thank you for your response. If I wanted to calculate the surface area of
this cortical ROI, would i pass lh.area.pial into ? Do i still use
--accumulate flag?

Thank you,

Carlos

On Thu, Jun 15, 2023 at 5:17 PM Huang, Yujing 
wrote:

> External Email - Use Caution
>
> Hi Carlos,
>
>
>
> Your commands look correct to calculate mean cortical thickness.
>
>
>
> To calculate the total volume, pass lh.volume to –in <>, and specify
> –accumulate on the command line: *MailScanner has detected a possible
> fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1VurGVMn29VBCV4gEY-1urMHf0Tc2Q5K6l_Q9RtFkHSD4boTU7uMNAd9KSB9eY23wb5F5JkZVhaKJ0aehfz-K1kXaPch5YcDhLo5NOKxM_huiMH0dpH5Y2hnfxkP-WVuCU6m7-1MwV0y6qQNmYPwMr3GEaRVIbLjBKZY1ASWWOW-eS7P-SKIOQ4nJY7cm4rE-x8RdyQWmQZQ0GZkq8ZeS8dHvTUWQ7jhT3QK13LbHNncTYLUhxMjeydJBdlBjqGqG8bCjQ-hdGTadf6DXCo6Bn559C9L2HGyX4hX0oSp1WBQiKqRR7g5GiWpdZHJb_-ZB/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats
> <https://secure-web.cisco.com/1GYp9YVgT3IIE67jb48sFXaEizpNOJyZRUgKL5vDUwx_U39xxjrLMFBNhTxtj7sMD3dgS4Fi-KQqcsDOLk6tnscZfUR_d5_jnsH4q5mi8mxDjYdGmFfVO1DWbCEAFdW3FZXJddre4EsMQe72s-ietR9ptbeXYa5yp5WL-1KVIwGGK_F8BHpxojM6BS4lqEhT8Mg2Z_-YJa27XiX1WhmK9jYL1vaM4PQ4Fe8kcDmkB24698-WNPLqid3met5WuTLAWwkKUA6ELeeuG394Gl8yHGA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats>
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer
> *Sent:* Thursday, June 15, 2023 11:36 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Calculate cortical thickness of a volumetric ROI
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
> I am trying to calculate the cortical thickness of a volumetric ROI that I
> created that I have in subject space for every subject in my dataset. I was
> using *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1pXTMCre1AsCZTEIbgrEJaknmPI8CmxkcdA4Wms31XfrQ9ENPg5XK0K7sTORK5BoKjzRhCLOEl7f2o4k5zolqfiJGu4xLzdTBbsb07maqI0XVXkw4LfzMdpk3SGUrc2PWBF9e-LbCA4129qWNpBZNMpoI1267ojoE_RAylNZI1f6HwDLSSFlDZn2-fH02MtRk_Dw9qrx1HguntVrowlahx0zmqnjD8VZO4auFqCeUKkbpvZUE1opoJiGsMq0hcJpokWUHiCJB2FjGjH4k-m_qK6TsRHpfTVQ8Nce43QMsEP9uIE7hVI9G-v4inWZNV0OO/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness
> <https://secure-web.cisco.com/1Z5OP8XDp2iTZo4YMybrzCFH9SwKBzyQx9vsSEFhl_f6qfhbWsl0xhAi5bYwjQG5MHh7ZBs9ADbhhnZ29DoSVWVVo5AquAm8aIde3IMQMJt9EBOhJ7ZoVI_JUHIYeCdpKAP5_-cZrBLflOE536wS6M31OKaD4bqQsKfG_furvWZ4uDamocw-yUSMKK2QadGa8bUJRw5TZn9pFhy_5xypbEQZ2g25BUdE17bxwUOwwlW1dD_5ekqmwY3sClBqLaWqGJVepW7LfU0bIa2D_8DfcDkx7Bkbp-YS_5h1d5YXXY_pOh7wAebQPQQmZxXhkixsQKQBwYfdv0BEthv-Pp5S9oQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness>
> as a guide.
>
> Since, I already have the volumes in subject space. I did a modified
> pipeline and only did the following for each subject:
> 1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1
> --interp nearest --hemi lh --out lh.ROI5.mgh
> 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in
> lh.thickness --sum segstats-ROI5.txt
>
> Does this make sense? Also, separately, is the volume that is also
> computed in this method accurate? I noticed that the volume is always equal
> to the number of voxels, which I assume a voxel is equal to 1mm^3? However,
> when looking at aseg.stats these volumes have different values from their
> number of voxels.
>
> Thank you,
>
> Carlos
>
>
>
>
>
>
> ___
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Re: [Freesurfer] Asymmetry analysis

2023-07-03 Thread Carlos Alcocer 
External Email - Use Caution

Thank you. I guess I am still confused on how to actually get results to
visualize. I would like to assess left-right hemispheric cortical asymmetry
. Ideally, i would like the analysis to be paired (ie. L vs R for each
subject, rather than the average of L vs average of R across subjects). How
would I go about analyzing and visualizing this in freesurfer using
xhemi. Also is there a way to this with a ROI rather than the whole brain?

Thanks,

Carlos

On Tue, Jun 20, 2023 at 9:26 AM Douglas N. Greve 
wrote:

> External Email - Use Caution
>
> That map is whatever you are studying. Eg, lh.thickness
>
> On 5/25/2023 1:30 PM, Carlos Alcocer wrote:
>
> External Email - Use Caution
> Hello,
>
> I am trying to do an asymmetry analysis using steps detailed in *MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be* 
> https://secure-web.cisco.com/1_yNnJ9fMi64wWs9Ha4WPhzOEIiP_nSgP3fNcqEdlPAUTHBsMormRtH1uG7T4xSV4GYb3fuvVu9HPdEeEcoLi7p4OX6TiXtjcba8MO0vbTMWhRoATdv7gJo5go_xcxF5BofFGAHkEGU2MQVoUTW1iMNROeneLdTxINLgvUVYJ5PJxittYfUIATJLBwd6KcTTR02GGhXKniBllSqVJRxrOqJe5P0so_97JPwLiaeR6-cOS4jGGmm0YgLa0S9yMyQOACu-JQGfuO3K8oExEMIw78330TuXBdcdeRX1aHB0vrLhMM_febq4aiKTW5u0gj4EA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FXhemi
> <https://secure-web.cisco.com/1E9BKFPFixB_mpRwvgfFNlEN0qYfJdo8MVLo6aeqDf-afyiae0jseDSkmT4rjZVPVW2YddkoaVShtXUvmMsZD2Q-O-EMrqoRl9tSf1WZdkCT-CHkbB5CF1uzhSSh52snNjiVSUe06Hglkpgu0zWkav2vu-QdQ9SI82oqSGVYhDWH2OrUtc9r-If8eYFj3engrDG1rTdNx-nUlQfLR4sDnC7xSGjz5joW_VQ91mx5zoRqiJRipABc1J_XyomlcuybTD_qYerY4spWepy4DYT69qhv4ush_fMBBytkxd2h1sE4pHwpxMg_BUR5CoVcqKGPclpe-J-6ZS5kwFL7RnVDnXg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FXhemi>
>
> However, step 1.3 starts with running:
>
> mris_apply_reg --src lh.map.mgh --trg lh.map.lh.fsaverage_sym.mgh
> --streg $SUBJECTS_DIR/subject/surf/lh.fsaverage_sym.sphere.reg
> $FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg
>
> What is this lh.map.mgh file? and where can I find it/how can i make it?
>
> Thank you,
>
> Carlos
>
>
>
>
> ___
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>  .
> Please note that this e-

[Freesurfer] Calculate cortical thickness of a volumetric ROI

2023-06-15 Thread Carlos Alcocer 
External Email - Use Caution

Hello,

I am trying to calculate the cortical thickness of a volumetric ROI that I
created that I have in subject space for every subject in my dataset. I was
using 
https://secure-web.cisco.com/1Z5OP8XDp2iTZo4YMybrzCFH9SwKBzyQx9vsSEFhl_f6qfhbWsl0xhAi5bYwjQG5MHh7ZBs9ADbhhnZ29DoSVWVVo5AquAm8aIde3IMQMJt9EBOhJ7ZoVI_JUHIYeCdpKAP5_-cZrBLflOE536wS6M31OKaD4bqQsKfG_furvWZ4uDamocw-yUSMKK2QadGa8bUJRw5TZn9pFhy_5xypbEQZ2g25BUdE17bxwUOwwlW1dD_5ekqmwY3sClBqLaWqGJVepW7LfU0bIa2D_8DfcDkx7Bkbp-YS_5h1d5YXXY_pOh7wAebQPQQmZxXhkixsQKQBwYfdv0BEthv-Pp5S9oQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness
as a guide.

Since, I already have the volumes in subject space. I did a modified
pipeline and only did the following for each subject:
1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1
--interp nearest --hemi lh --out lh.ROI5.mgh
2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in
lh.thickness --sum segstats-ROI5.txt

Does this make sense? Also, separately, is the volume that is also computed
in this method accurate? I noticed that the volume is always equal to the
number of voxels, which I assume a voxel is equal to 1mm^3? However, when
looking at aseg.stats these volumes have different values from their number
of voxels.

Thank you,

Carlos
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[Freesurfer] Calculate cortical thickness of a volumetric ROI

2023-06-07 Thread Carlos Alcocer 
External Email - Use Caution

Hello,

I am trying to calculate the cortical thickness of a volumetric ROI that I
created that I have in subject space for every subject in my dataset. I was
using 
https://secure-web.cisco.com/1SRB1kl1prYOxcV3133JRM9O5Bj21w9M9aZYfcod7MM5GHwsDfBpkAJGh0Rs610J3N7kmx2WIaftk4KvSgiCc24mytynSAJYbOtgdbThjndntDX62ycHQTnGr8XWqmgIlVYB94HendZy03fCZG5yog4ttjg6kDqoW7EMD3euPhVAH7RWYjLA4o21LgNH2gGJ8OiUAGmi9PDXP978HKFgSGmlgfGg_ZJWDmZ0AywDyaN3_J1mfdwUSoJGMkUKKRrSzZmQSwHFkS0pWWyNllEn3RWBzI56yvVh7FGRHcpVI7U_3QPzsgdfeYX5LRKxg_kwErt-McsKT97BlE8Lj5Yo9xQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness
as a guide.

Since, I already have the volumes in subject space. I did a modified
pipeline and only did the following for each subject:
1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1
0.1 --interp nearest --hemi lh --out lh.ROI5.mgh
2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in
lh.thickness --sum segstats-ROI5.txt

Does this make sense? Also, separately, is the volume that is also computed
in this method accurate? I noticed that the volume is always equal to the
number of voxels, which I assume a voxel is equal to 1mm^3? However, when
looking at aseg.stats these volumes have different values from their number
of voxels.

Thank you,

Carlos
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[Freesurfer] Asymmetry analysis

2023-05-25 Thread Carlos Alcocer 
External Email - Use Caution

Hello,

I am trying to do an asymmetry analysis using steps detailed in
https://secure-web.cisco.com/1E9BKFPFixB_mpRwvgfFNlEN0qYfJdo8MVLo6aeqDf-afyiae0jseDSkmT4rjZVPVW2YddkoaVShtXUvmMsZD2Q-O-EMrqoRl9tSf1WZdkCT-CHkbB5CF1uzhSSh52snNjiVSUe06Hglkpgu0zWkav2vu-QdQ9SI82oqSGVYhDWH2OrUtc9r-If8eYFj3engrDG1rTdNx-nUlQfLR4sDnC7xSGjz5joW_VQ91mx5zoRqiJRipABc1J_XyomlcuybTD_qYerY4spWepy4DYT69qhv4ush_fMBBytkxd2h1sE4pHwpxMg_BUR5CoVcqKGPclpe-J-6ZS5kwFL7RnVDnXg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FXhemi

However, step 1.3 starts with running:

mris_apply_reg --src lh.map.mgh --trg lh.map.lh.fsaverage_sym.mgh
--streg $SUBJECTS_DIR/subject/surf/lh.fsaverage_sym.sphere.reg
$FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg

What is this lh.map.mgh file? and where can I find it/how can i make it?

Thank you,

Carlos
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[Freesurfer] Volume transformation issue

2023-05-18 Thread Carlos Alcocer 
External Email - Use Caution

Hi,

I am trying to transform a volumetric ROI from MNI152 space to native
space. I am doing this in 2 steps. First (1) I am creating a registration
file using bb register to create a registration file and then (2) I am
using mri_vol2vol to transform volume onto my subject using the
registration file I created in step 1.

1. bbregister --s subjid --mov roi_in_MNI152.mgz --t1 --reg register.dat

2. mri_vol2vol --targ subjid/mri/T1.mgz --mov roi_in_MNI152.mgz --reg
register.dat --o roi_in_native.mgz

However, the transformed volume is not anatomically positioned where it is
supposed to be. Is there an error in my method?

Thank you,

Carlos
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[Freesurfer] register to mni space

2023-04-21 Thread Carlos Alcocer 
External Email - Use Caution

I registered a subject to mni space using the mri_cvs_register command with
the --mni flag. However, the output files do not include a new
aparc.a2009s+aseg.mgz. I wanted this atlas overlayed on the mni registered
subject so I could extract one of the labels. Is this possible?

Thanks,

Carlos
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Re: [Freesurfer] creating average labels

2023-04-20 Thread Carlos Alcocer 
External Email - Use Caution

I am basically looking for a way to create an average of the labels for the
L  subcallosal cingulate cortex (SCC) and then make an average of the
labels for the R SCC across all subjects  and use these 2 average labels as
a mask to see if the average label L SCC and average label of R SCC aligns
well with with the actual location of the L and R SCC for each individual
subject. Do you know of a better way to do this?

On Thu, Apr 20, 2023 at 9:19 AM Huang, Yujing 
wrote:

> External Email - Use Caution
>
> Hi Carlos,
>
>
>
> mri_concat concatenates input .mgz files.
>
>
>
> The following command will output C.mgz with A.mgz as the first frame, and
> B.mgz as the second frame, assuming both A and B have only one frame.
>
> mri_concat --i A.mgz --i B.mgz --o C.mgz
>
>
>
> I’m not sure that is what you are looking for.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer
> *Sent:* Wednesday, April 19, 2023 1:02 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] creating average labels
>
>
>
> *External Email - Use Caution*
>
> Good afternoon,
>
>
>
> I would like to verify that the subcallosal cingulate cortex (SCC)
> segmentation of my subjects are correct. I want to do this by creating an
> average label of the left SCC and an average label of the right SCC which I
> can then map onto each subject.
>
>
>
> If I save these labels from each subject as a volume (.mgz) and then run
> mri_concat on the left SCC labels (.mgz) and then on the right SCC labels
> (.mgz), would this accomplish my desired goal?
>
>
>
> Tks,
>
>
>
> Carlos
>
>
>
>
> ___
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>  <
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>  .
> Please note that this e-mail is not secure (encrypted).  If you do not
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>


-- 
Carlos Alcocer
B.A. Neurobiology and Behavior, Cornell University, 2019
818-746-0302
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[Freesurfer] creating average labels

2023-04-19 Thread Carlos Alcocer 
External Email - Use Caution

Good afternoon,

I would like to verify that the subcallosal cingulate cortex (SCC)
segmentation of my subjects are correct. I want to do this by creating an
average label of the left SCC and an average label of the right SCC which I
can then map onto each subject.

If I save these labels from each subject as a volume (.mgz) and then run
mri_concat on the left SCC labels (.mgz) and then on the right SCC labels
(.mgz), would this accomplish my desired goal?

Tks,

Carlos
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[Freesurfer] T1 with contrast

2023-04-07 Thread Carlos Alcocer 
External Email - Use Caution

Can you use T1 with contrast in freesurfer or does it have to be
non-contrast images?

Tks,

Carlos
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[Freesurfer] Subcallosal cingulate cortex segmentation/parcellation

2023-04-06 Thread Carlos Alcocer 
External Email - Use Caution

Hi,

I am interested in the aparc+aseg stats for the subcallosal
cinuglate cortex (SCC). When learning freesurfer, the lectures/tutorials
mention not to make manual edits to medial structures which I believe would
include the SCC.

Will the stat output files still be accurate if I don't make edits to these
areas given that the surfaces can look quite messy in those areas at times?

Thank you,

Carlos
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[Freesurfer] Autrecon-pial command

2023-03-29 Thread Carlos Alcocer 
External Email - Use Caution

Hello all,

Does -autorecon-pial flag also recreate the statistics tables with the new
surfaces? or do you have to run autorecon3 after to recalculate stats files?

Tks,

Carlos
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Re: [Freesurfer] Freeview Edit options restricted

2023-03-07 Thread Carlos Alcocer 
External Email - Use Caution

Also is it possible to not archive or not include email signature on that
reply email. didn't mean to have my email signature on there

On Tue, Mar 7, 2023 at 12:30 PM Carlos Alcocer  wrote:

> Thank you for your prompt response. Yes, while it does not show the brush
> size and certain menu options being grayed out, when I hover the cursor
> over these options the cursor becomes grayed out and it does not let me
> click on any options. For example if I clicked the brush size nothing would
> happen.
>
> Thank you,
>
> Carlos
>
> On Tue, Mar 7, 2023 at 12:11 PM Wang, Ruopeng 
> wrote:
>
>> Recon Edit mode will disable a few options. But it looks to me the Brush
>> Size is not grayed out from your screenshot.
>>
>> To close the window, you can just switch to Navigate mode.
>>
>> Ruopeng
>>
>> On Mar 7, 2023, at 11:34 AM, Carlos Alcocer  wrote:
>>
>> External Email - Use Caution
>>
>> Hello,
>>
>> When I try to do recon-edit, it does not let me click on certain options
>> ie. changin the brush size. It additionally doesnt let me exit out of or
>> minimize it. I am running the most recent version of freesurfer (7.3.2) on
>> linux (wsl). I reinstalled/updated freeview but this did not resolve the
>> issue. I have attached screen shot below. You cant see cursor but if i were
>> to hover over brush size for example, the cursor would be a light gray and
>> not let mec change any of the options.
>>
>> 
>>
>> Thank you,
>>
>> Carlos
>>
>>
>>
>> ___
>> Freesurfer mailing list
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>>
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>
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Re: [Freesurfer] Freeview Edit options restricted

2023-03-07 Thread Carlos Alcocer 
External Email - Use Caution

Thank you for your prompt response. Yes, while it does not show the brush
size and certain menu options being grayed out, when I hover the cursor
over these options the cursor becomes grayed out and it does not let me
click on any options. For example if I clicked the brush size nothing would
happen.

Thank you,

Carlos

On Tue, Mar 7, 2023 at 12:11 PM Wang, Ruopeng 
wrote:

> Recon Edit mode will disable a few options. But it looks to me the Brush
> Size is not grayed out from your screenshot.
>
> To close the window, you can just switch to Navigate mode.
>
> Ruopeng
>
> On Mar 7, 2023, at 11:34 AM, Carlos Alcocer  wrote:
>
> External Email - Use Caution
>
> Hello,
>
> When I try to do recon-edit, it does not let me click on certain options
> ie. changin the brush size. It additionally doesnt let me exit out of or
> minimize it. I am running the most recent version of freesurfer (7.3.2) on
> linux (wsl). I reinstalled/updated freeview but this did not resolve the
> issue. I have attached screen shot below. You cant see cursor but if i were
> to hover over brush size for example, the cursor would be a light gray and
> not let mec change any of the options.
>
> 
>
> Thank you,
>
> Carlos
>
>
>
> ___
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-- 
Carlos Alcocer
B.A. Neurobiology and Behavior, Cornell University, 2019
818-746-0302
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[Freesurfer] Freeview Edit options restricted

2023-03-07 Thread Carlos Alcocer 
External Email - Use Caution

Hello,

When I try to do recon-edit, it does not let me click on certain options
ie. changin the brush size. It additionally doesnt let me exit out of or
minimize it. I am running the most recent version of freesurfer (7.3.2) on
linux (wsl). I reinstalled/updated freeview but this did not resolve the
issue. I have attached screen shot below. You cant see cursor but if i were
to hover over brush size for example, the cursor would be a light gray and
not let mec change any of the options.

[image: image.png]

Thank you,

Carlos
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 .
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[Freesurfer] Freeview Installation Error

2023-02-14 Thread Carlos Alcocer 
External Email - Use Caution

Hi,

I have been trying to install FreeSurfer and I went to test out the
freeview command but received the following error.

freeview: error while loading shared libraries: libGL.so.1: cannot open
shared object file: No such file or directory

I am unsure how to proceed.

Thank you,

Carlos
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