Re: [Freesurfer] Distance Measurement After recon-all

[John Anderson]

External Email - Use Caution

Dear Freesurfer Experts,
I would like to inquire if there is a FreeSurfer command that allows me to
measure the distance (in voxels or mm) between a lesion mask (output of
samseg) and the closest voxels in the ribbon after applying "recon-all" to
T1 images. If there is no such command, I am considering measuring the
center of the lesion mask and calculating the distance between this center
and every voxel in the closest parcel in the ribbon, then selecting the
shortest distance. i'm not sure if this is the correct approach so I
appreciate your suggestions.
Thank you
John

On Mon, Nov 20, 2023 at 7:13 AM John Anderson  wrote:

> Dear FreeSurfer experts, I would like to know if there is a command in
> FreeSurfer that can help me measure the distance (in voxels or mm) between
> a lesion mask and the closest voxels in the ribbon after applying recon-all
> to T1 images. Thanks for your advice
>
> John
>
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[Freesurfer] Distance Measurement After recon-all

[John Anderson]

External Email - Use Caution

Dear FreeSurfer experts, I would like to know if there is a command in
FreeSurfer that can help me measure the distance (in voxels or mm) between
a lesion mask and the closest voxels in the ribbon after applying recon-all
to T1 images. Thanks for your advice

John
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Re: [Freesurfer] data quality check before analysis [EXTERNAL]

[John Anderson]

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It doesn't matter, just make sure to be consistent. Use the same system,
the same computer setup, and the same system version, etc. Analyzing data
in parallel is always recommended with large sample sizes like yours


** External Email - Caution **

External Email - Use Caution
Thank you for your response. My next question is regarding the analysis
process. I am curious to know if there is any difference between analyzing
one specific subject and analyzing multiple subjects in parallel. For
instance, if I am working on 1000 subjects, would it make a difference in
the volumetric results if I analyze all of them at once in parallel or
break them down into smaller groups to analyze? I would greatly appreciate
your help with this.

Thank you and Best Regards,
Yunus.




*Yunus Soleymani*

*Ph.D. Candidate of Neuroimaging *
*Tehran University of Medical Sciences*

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On Saturday, October 14, 2023 at 03:29:11 PM GMT+3:30, John Anderson <
jb19790...@gmail.com> wrote:


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- For versions 7+, use the following executable to compute QA stats
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Re: [Freesurfer] data quality check before analysis [EXTERNAL]

[John Anderson]

External Email - Use Caution

- FreeSurfer 5.3 QA Tools 
https://secure-web.cisco.com/1xhhgMhrQlSBmGkb8NMn06KLlNRaz3DnQ7vzdZdQzrqjoeDsU5-gpo8VaUCxtX79W2O5j9rC87MnVFoBXzpHmSrCDzkZXGGR7I_PmSZlic0yw_BJBu2NDNAuQxkdpXtMPVHqiMbinZ5ak8HWwws2ZWPYgfTlbVjDSje40bRgu0R5XIZ3hox3WQjltQwACheB5Jq32Mma-tb_TqdU4lsjmK09zly52yDwCAHO5fRp45UbD9lyo45IyXqFzNllJDwqW-nV1LmciahyfMxkeRoIhvFEjQvJopXYiXVMQZipMiNsF89zddc8O_x38B-Stc-cn3pKMhb5WTqfyKepybZXKSqs6FQMvc7XUNsSo3yAoaSs/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FQATools
- For versions 7+, use the following executable to compute QA stats
https://secure-web.cisco.com/176EEDJE8rR684nmHeoPJAc8XhajsuDydGl4DaVSEQrq7SFq6berFEZvvOdBTdao2mTaLlsLbU-w8g5Dp_665W5VCUWfLiNclcg0KGiypCKQUvy4TGV_tkCZwf--67mFfszR5qBeBwZPULZs3PKZ7CFx8Kzlk9wJZG3VXdeKhD4OxGTYzCHEGXC_kU5OIEhETXbAouQJz7T3F3a1zdXc8w3AFmgNePUHEt6NxeiHtftxbrkOXTcP62a3VrFvnxTrOKTCuMi6PwyLJUveVXKrsYBjxeK3tbvFmc2TGfHx0EMpV4TW_MqtNBnNQM6Vjl9KD1EH7RVEVrMGX1Vlh3McyA6xERxZhnerg3YM1tBMSCgg/https%3A%2F%2Fgithub.com%2FDeep-MI%2Ffsqc

Be aware that there are NO alternatives to visual inspection

--
*From:* freesurfer-boun...@nmr.mgh.harvard.edu <
freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of yunus soleymani <
soleymani.yu...@yahoo.com>
*Sent:* Saturday, October 14, 2023 3:18 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [Freesurfer] data quality check before analysis [EXTERNAL]

** External Email - Caution **

External Email - Use Caution

Hi there,

My name is Yunus and I'm currently working on my Ph.D. thesis, which
involves analyzing the HCP database volumetrically using Freesurfer.
However, before I begin with the software, I was wondering if there is a
tool in Freesurfer that can perform a quality check on the data to identify
any possible artifacts or noise that might affect the analysis.

Could you please let me know if such a tool exists in Freesurfer? Your help
would be much appreciated.

Thank you and Best Regards,
Yunus.



*Yunus Soleymani*

*Ph.D. Candidate of Neuroimaging *
*Tehran University of Medical Sciences*

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Re: [Freesurfer] mri_glmfit-sim - Clusterwise correction for multiple comparisons.

[John Anderson]

External Email - Use Caution

assuming that all preprocessing steps, fsgd file and contrasts are correct,
the choice between doss and dods could explain some of the variability
you're seeing in your results. Consider running both models and possibly
additional validation to see which model better fits your data. Each model
assumes a different relationship between your groups and covariates, and
they can yield different results because of these assumptions.
DOSS: In this model, the assumption is that all groups are affected by the
covariates in the same way, i.e., they have the same slope but may have
different intercepts. Essentially, it assumes that the effect of your
covariates (age, depression, anxiety) is constant across all groups. Any
variability among groups will be captured in the intercept term.
DODS: This model allows each group to have a different relationship with
the covariates. It assumes that both the slopes and the intercepts can
differ across groups. In this case, not only can the groups differ in terms
of their mean values (offset), but they can also differ in how they relate
to the covariates (slope).
If you use DOSS but the truth is more akin to DODS, you might underestimate
the variability in the relationships between groups and covariates, which
could potentially lead to the kinds of inconsistencies you've observed.
Conversely, choosing DODS when DOSS would be sufficient could introduce
unnecessary complexity and consume degrees of freedom, which might affect
the statistical power.
Given your focus on nuances like controlling for age, depression, and
anxiety, it would be worth scrutinizing how these covariates interact with
your groups. If you suspect different groups could indeed have a different
relationship with these covariates, DODS might be more appropriate.
Finally, The results you are observing appear to be false positives, likely
due to the use of a lenient statistical significance threshold in your
surface-based analysis. Opting for a more rigorous threshold, such as a
cache=4, is generally a solid choice, particularly when you don't have a
specific hypothesis about the location of significance of correlation and
are conducting exploratory analyses

On Fri, Sep 29, 2023 at 3:38 PM Guthrie, Andrew J. <
ajguth...@mgh.harvard.edu> wrote:

> External Email - Use Caution
>
> Hi all,
>
>
>
> I took the freesurfer course in the recent past, and I am now beginning to
> run some glm thickness analyses!
>
>
>
> Currently I am doing a thickness analysis looking at the difference
> between two groups while controlling for age, and two continuous measures
> of depression and anxiety. The general commands I run are as follows:
>
>
>
> mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage
> --target fsaverage --hemi lh --o lh.[filename].thickness.10.mgh
>
> mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage
> --target fsaverage --hemi rh --o rh.[filename].thickness.10.mgh
>
> mri_glmfit --y lh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss
> --C contrast.mtx --surf fsaverage lh --glmdir lh_[filename]_fwhm10.glmdir
>
> mri_glmfit --y rh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss
> --C contrast.mtx --surf fsaverage rh --glmdir rh_[filename]_fwhm10.glmdir
>
> mri_glmfit-sim --glmdir lh_[filename]_fwhm10.glmdir --cwpvalthresh .05
> --cache 2.0 abs --2spaces
>
> mri_glmfit-sim --glmdir rh_[filename]_fwhm10.glmdir --cwpvalthresh .05
> --cache 2.0 abs --2spaces
>
>
>
> I noticed that in some analyses there would be no significant clusters
> when the threshold is set at 2.0 (p<0.01) but if you were to run the same
> analyses with a threshold at 2.3 (p<0.005) there would be a significant
> cluster, in the lingual for example. If I go one step further and set the
> threshold to 3.0 there is also a significant cluster – however the cluster
> is now in the isthmuscingulate.
>
>
>
> Am I doing something incorrectly or is this possible? And if so, could you
> help me understand what is going on here.
>
>
>
> Best,
>
>
>
> Andrew
>
>
>
>
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Re: [Freesurfer] mri_synthmorph

[John Anderson]

External Email - Use Caution

Dear Malte
Thank you so much. I've tried both rigid and affine transformations, and
I've attached a snapshot that shows how the CC doesn't fully overlap with
the template. I'm using a high-quality DTI image and am wondering if
incorporating a T1 image would help improve the registration. I'm not sure
how to apply a two-step registration, if that's even possible, using
mri_synthmorph. Thanks for your guidance.

Best,
John

On Fri, Sep 1, 2023 at 1:27 PM Hoffmann, Malte,PhD <
mhoffm...@mgh.harvard.edu> wrote:

> External Email - Use Caution
>
> Hi John,
>
> Currently, the default transformation model is "deform". Could you check
> if "affine" yields a better result?
>
> mri_synthmorph -m affine fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz
>
> Cheers,
> Malte
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of John Anderson <
> jb19790...@gmail.com>
> Sent: Friday, September 1, 2023 12:45
> To: Freesurfer support list
> Subject: [Freesurfer] mri_synthmorph
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
> I processed DTI data using dt_recon, and I want to register FA images to
> the standard MNI152 space. However, after running the command
> mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz,
>
> the registration is not accurate. I'm not sure what I've done wrong. Thank
> you for any guidance.
>
> sincerely
> J
>
>
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> e-mail contains patient information, please contact the Mass General
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>  <
> https://secure-web.cisco.com/1OhLWc08Q0-Z6vg0PUzLX0EzcQ1aYGzygiuxmzGiyBmXugoLvVDxNIQVmG3yRg2vuFBIYxJfBtpdNyRPBagy-SY8JibbuSTJRSOm60WYT_ZsTW_JbPpHbQrHVLpYuKC4oA4kbVsItWqHb1l2AvuQY_SlsQXRMPChkvYwjVUgo8Ym3nmhMI_PveVKy5jOUrg7OtQS-IwdiOrvN8Av9zQlfXDopDCJCMWPEvQ2LwWkhr833wO5mbJuywZtaPTQxuLx6K9P-0t2atHwUkh_44uMcKbgxOuI8oa4uPBoRvNyOjZIUHXm848FupEiJguWTPS2IY-4SD8jfui05l4_ZHXEFoQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>
>
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[Freesurfer] mri_synthmorph

[John Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I processed DTI data using dt_recon, and I want to register FA images to
the standard MNI152 space. However, after running the command
mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz,

the registration is not accurate. I'm not sure what I've done wrong. Thank
you for any guidance.

sincerely
J
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Re: [Freesurfer] Size of overlap between a label and a volume

[John Anderson]

External Email - Use Caution

Let's say the red spot is overlay.nii.gz
1) convert aparc+aseg from mgz to nii.gz using:
mri_convert aparc+aseg.mgz aparc+aseg.nii.gz
2) create mask between overlay and the atlas using fslmaths:
fslmaths aparc+aseg.nii.gz -mas overlay.nii.gz overlay_overlap.nii.gz
3) use fslstats (or mris_cacl) to compute volume:
fslstats   aparc+aseg.nii.gz -k overlay_overlap.nii.gz -V
this output #voxels and volume

Alternatively, you might consider mri_seg_overlap
https://secure-web.cisco.com/1yEdORqlIEup_8SwhRxwcP4XoV0QdvHT3rxvRNSBm4KwTJa8GFaC4IypTfW6sCwqLkCV8-04lx4IwpYw1bloRw_V6dP7ZHDGcAKW_GxvmcPnNpEDrGOUP0_IOqBySvJcnPNi6vhkSVi10dToaEBiERpqDFz-EnxCjEgNGIJ3XNt-k3tKuVVXCHwRVILgioT9OGbo6ypjpXFGP3ZXbaHEcno4FQfRfil7Daqyt9jtk6hu7MV49cAA-kVltRnz0XNs6FPf7MtEN0eemFGiV1vvMIp5rjRfhyA2LWaKuhK4F6Eq2uHqE_n9TYs6AsXPSvtrmL8vi3cGm-6XyMKJwBQAM1Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_overlap


On Fri, Jun 16, 2023 at 10:37 PM parsa...@student.ubc.ca <
parsa...@student.ubc.ca> wrote:

> External Email - Use Caution
>
> Hello,
>
> Hope you are doing well. I'm new to freesurfer so I was wondering if you
> could help me out with something please.
>
> I'm looking for a simple way to find the size (i.e. volume in mm3) of
> overlap between a particular label (1027 ctx-lh-rostalmiddlefrontal) ) in
> an aparc+aseg file and a NIfTI volume file that can be overlayed on the
> aparc+aseg file. Please look at the attached file for a better
> visualization of what I'm describing.
>
> I'd really appreciate it if you could point me in the right direction.
>
> Thank you,
>
> Parsa
>
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>  .
>
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[Freesurfer] Fwd: questions about mri_normalize

[John Anderson]

External Email - Use Caution

Dear experts,
I have been using the mri_normalize in FSv7.3.2 to standardize the
intensity of FLAIR images , and I've observed that increasing the sigma
parameter up to 25 is effective in improving the quality of the normalized
images for noisy datasets.
mri_normalize -sigma 25 -g 1 FLAIR_skullstripped.nii
FLAIR_skullstripped_norm.mgz

However, I have questions about the n argument, which is set to 2 by
default. For noisy images, white matter intensity after normalization is
around 140-150. When using n=10, I noticed that the white matter intensity
decreased from 140-150 to around 110-120, resulting in better quality
normalized images.
1) I'm wondering if there is a cut-off value for the number of iterations,
or if a higher number of iterations always yields better results.
2) Also, if the intensity of the white matter after normalization is not
around 110, but instead around 140 or 150, does that indicate that the
normalization was not effective and that we need to increase the number of
iterations?

Thank you for your assistance.
John
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[Freesurfer] questions about mri_normalize

[John Anderson]

External Email - Use Caution

Dear experts,
I have been using the mri_normalize in FSv7.3.2 to standardize the
intensity of FLAIR images , and I've observed that increasing the sigma
parameter up to 25 is effective in improving the quality of the normalized
images for noisy datasets.
mri_normalize -sigma 25 -g 1 FLAIR_skullstripped.nii
FLAIR_skullstripped_norm.mgz

However, I have questions about the n argument, which is set to 2 by
default. For noisy images, white matter intensity after normalization is
around 140-150. When using n=10, I noticed that the white matter intensity
decreased from 140-150 to around 110-120, resulting in better quality
normalized images.
1) I'm wondering if there is a cut-off value for the number of iterations,
or if a higher number of iterations always yields better results.
2) Also, if the intensity of the white matter after normalization is not
around 110, but instead around 140 or 150, does that indicate that the
normalization was not effective and that we need to increase the number of
iterations?

Thank you for your assistance.
John
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Re: [Freesurfer] mri_glmfit correction across lobes

[John Anderson]

External Email - Use Caution

Dear Dr Greve,
Apologize for not providing a clear explanation earlier. The file
lh.all.suvr.sm05.proj0.5.nii.gz is the result of combining all SUVR maps,
using mri_concat, after projecting them onto the brain surface with
mri_vol2surf.
I would like to know if it is possible to use mri_glmfit-sim to correct for
specific regions of interest (such as lobes) instead of correcting the
entire brain.
I am using the following command: mri_glmfit-sim --glmdir lh.suvr.glmdir
--cache 4 pos --cwp 0.05 --2spaces

When I include the "--annot lobes" option in my command (mri_glmfit-sim
--glmdir lh.suvr.glmdir --cache 4 pos --cwp 0.05 --2spaces --annot lobes),
the resulting statistical output is similar, but the annotations are
replaced with their corresponding lobes. However, p-values are not adjusted
for the number of regions of interest specified in the "--annot" option.
Thanks again

On Wed, Apr 5, 2023 at 10:46 PM Douglas N. Greve 
wrote:

> What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from? The name
> looks like it might be a voxel-wise map, but you say something about ROIs.
> mri_glmfit does not correct for multiple comparisons. For ROI-based
> analyses, you can use bonferroni or FDR. For maps you can use
> mri_glmfit-sim.
>
> On 4/4/2023 4:53 PM, John Anderson wrote:
>
> External Email - Use Caution
> Hello Freesurfer,
> Currently, I am using the Petsurfer manual, which is easily understandable
> and clear. Nonetheless, I have a question regarding the "mri_glmfit" step.
> As far as I know, this command is used to correct data for multiple
> comparisons among all the ROIs in the aparc+aseg.mgz file. Can you please
> confirm if my understanding is correct?
>
> mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd 2G0C.fsgd --C
> patients_vs_controls.mtx --surf fsaverage lh --cortex --glmdir
> lh.patinets_vs_controls
>
> In particular, I am interested in correcting data across lobes instead of
> across all ROIs. I followed the steps mentioned in the FS forum to create
> lobes, and I can observe lobe annotations in the wmparc.mgz file. I am
> curious to know whether using the "--annot" flag will adjust the p-values
> across different lobe ROIs instead of all ROIs in the aparc+aseg.mgz file.
> I have attempted this, but it appears to only change the name of the
> annotation in the final statistics file, and the p-value remains the same.
> Do I need to include any additional arguments in the command?
>
> Thanks for your help
> John
>
> ___
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>
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[Freesurfer] mri_glmfit correction across lobes

[John Anderson]

External Email - Use Caution

Hello Freesurfer,
Currently, I am using the Petsurfer manual, which is easily understandable
and clear. Nonetheless, I have a question regarding the "mri_glmfit" step.
As far as I know, this command is used to correct data for multiple
comparisons among all the ROIs in the aparc+aseg.mgz file. Can you please
confirm if my understanding is correct?

mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd 2G0C.fsgd --C
patients_vs_controls.mtx --surf fsaverage lh --cortex --glmdir
lh.patinets_vs_controls

In particular, I am interested in correcting data across lobes instead of
across all ROIs. I followed the steps mentioned in the FS forum to create
lobes, and I can observe lobe annotations in the wmparc.mgz file. I am
curious to know whether using the "--annot" flag will adjust the p-values
across different lobe ROIs instead of all ROIs in the aparc+aseg.mgz file.
I have attempted this, but it appears to only change the name of the
annotation in the final statistics file, and the p-value remains the same.
Do I need to include any additional arguments in the command?

Thanks for your help
John
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Re: [Freesurfer] mri_convert mosaic dicoms

[John Anderson]

External Email - Use Caution

Thank you, Dr Greve.  I tried it, but it didn't work. By 'didn't work,' I
mean that when I visualized the NIfTI file, I saw a line on the coronal and
sagittal planes, and the whole brain on the axial view. I was able to
generate a NIfTI image with multiple volumes as expected by using the
mri_convert command with the --nslices-override argument, but I'm not sure
if I'm using it correctly.

On Mon, Mar 27, 2023 at 11:19 AM Douglas N. Greve 
wrote:

> Can you try it with --dcm2niix ?
>
> On 3/25/2023 9:43 AM, John Anderson wrote:
>
> External Email - Use Caution
> Dear Dr Doug Greeve,
> For each participant in my dataset, I have 8 mosaic volumes with 36 slices
> each. I am trying to convert the DICOM files to Nifti format using the
> mri_convert command in FreeSurfer version 7.3.2. However, the conversion
> process fails even when using this latest dev version. To resolve this
> issue, I attempted to use the --nslices-override option. It seems working,
> however, I am unsure if I used it correctly, and I was not able to find any
> relevant examples or guidance on how to use this option in the FreeSurfer
> documentation or other websites.
>
> n=({-1..7})
> unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log
> for i in $(cat dicomdir.sumfile  | awk '{print $2}'); do
> n=$(($n + 1))
> mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n
> done
>
> Thanks for guidance,
> John
>
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>
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[Freesurfer] mri_convert mosaic dicoms

[John Anderson]

External Email - Use Caution

Dear Dr Doug Greeve,
For each participant in my dataset, I have 8 mosaic volumes with 36 slices
each. I am trying to convert the DICOM files to Nifti format using the
mri_convert command in FreeSurfer version 7.3.2. However, the conversion
process fails even when using this latest dev version. To resolve this
issue, I attempted to use the --nslices-override option. It seems working,
however, I am unsure if I used it correctly, and I was not able to find any
relevant examples or guidance on how to use this option in the FreeSurfer
documentation or other websites.

n=({-1..7})
unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log
for i in $(cat dicomdir.sumfile  | awk '{print $2}'); do
n=$(($n + 1))
mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n
done

Thanks for guidance,
John
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Re: [Freesurfer] mri_convert mosaic data

[John Anderson]

External Email - Use Caution

Thank you.
I would appreciate feedback from developers on two issues.
1) mri_convert in FS v6 is unable to convert any mosaic DICOMs to Nifti
format. In FS 7.3.2, mri_convert was able to convert mosaic DICOMs to Nifti
in some subjects but failed for many others. All subjects were scanned on
the same MRI scanner with the same acquisition parameters, and I am unable
to determine the cause of the issue.
2) I have 8 ASL mosaic volumes (36 slices) for each participant in my data.
When attempting to convert the DICOMs to Nifti using the simple mri_convert
  command, it fails. Is it correct to apply the
following steps?

n=({-1..6})
unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log
for i in $(cat dicomdir.sumfile  | awk '{print $2}'); do
n=$(($n + 1))
mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n
done

Thank for guidance,
John

On Wed, Mar 15, 2023 at 3:07 PM Huang, Yujing 
wrote:

> Hi John,
>
>
>
> I’m assuming all 64 DICOM files are in the same directory.
>
>
>
> Which Freesurfer version are you using? If you are using 7.3.2, can you
> try mri_convert -dcm2niix to convert those DICOMs? It will use dcm2niix to
> convert.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *John Anderson
> *Sent:* Wednesday, March 15, 2023 1:46 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] mri_convert mosaic data
>
>
>
> *External Email - Use Caution*
>
> Dear Freesurfer,
>
> I have ASL DICOM data from a Siemens scanner in mosaic format.
>
> For each subject, there are 64 DICOM files, which consist of both tags and
> controls.
>
> I would like to convert each individual DICOM into a separate NIfTI file
> or a single 4D NIfTI file ,composed of all 64 dicoms, using the
> mri_convert. However, when I use the command mri_convert input_dicom
> output_nifti, the output does not seem right, as it only displays one slice
> in the sagittal and coronal views. Could you please provide guidance on how
> to properly convert these DICOM files using mri_convert?
>
>
>
> Thanks very much
>
> John
> ___
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>  <
> https://secure-web.cisco.com/1bS_r7x5d5hARMp38OKVr578uECWvno1sIuXjsvMdCyKx8Izw4ectJDqcZrFYs8l7hyaF-kogGHnkRnh_I3S08KRJi3oH94EY22jVfDitccUj0nAt1ZHYctjjnSd6cbwjY9VqiO1jFGiHTrYP-sLTSy0EDKu7G_Mq-bVra71ZM8n6sOmcAvJgE7Gs2MXfAqlDQwJ6NX2yQ9hWBVt-uai_vLxq_Kd3rS9j9_dxokAcPVTt0zc16K9NXuiugAaFwmwKMyCLPHrFPnkCGDOqctYh1st7rVNaxcfhuhLuVCrJPyKTL57UOaD_yOvJP_qYVGqrbHv2Nfa3cbyDJMKZ8Ja5qg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>
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[Freesurfer] mri_convert mosaic data

[John Anderson]

External Email - Use Caution

Dear Freesurfer,
I have ASL DICOM data from a Siemens scanner in mosaic format.
For each subject, there are 64 DICOM files, which consist of both tags and
controls.
I would like to convert each individual DICOM into a separate NIfTI file or
a single 4D NIfTI file ,composed of all 64 dicoms, using the mri_convert.
However, when I use the command mri_convert input_dicom output_nifti, the
output does not seem right, as it only displays one slice in the sagittal
and coronal views. Could you please provide guidance on how to properly
convert these DICOM files using mri_convert?

Thanks very much
John
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[Freesurfer] mri_segstats

[John Anderson]

External Email - Use Caution

Dear Freesurfer community,
Please forgive me for the basic nature of my question.
I was wondering whether there is an argument that can be included in
mri_segstats to display the results in cubic centimeters (cm^3) instead of
cubic millimeters (mm^3). thanks for any suggestions.

Thank you, John
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Re: [Freesurfer] MRI image quality metrics

[John Anderson]

External Email - Use Caution

export SUBJECTS_DIR=

mri_cnr $SUBJECTS_DIR//surf/ $SUBJECTS_DIR/ 
/mri/norm.mgz > output_CNR.txt
wm-anat-snr --s  check stats/wmsnr.e3.dat  the output is
snr for the whole white matter.

if you need snr for every roi in aseg.stats or wmparc.stats, then you can
add the flag --snr to the command mri_segstats as follows:

mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz
--empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0
--excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
--surf-ctx-vol --totalgray --euler --ctab
/usr/local/freesurfer/6.0/ASegStatsLUT.txt --subject  --snr

do the same for wmparc.stats:
mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv
mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --subject 
--surf-wm-vol --ctab /usr/local/freesurfer/6.0/WMParcStatsLUT.txt --etiv
--snr

make sure to change /usr/local/freesurfer/6.0/ASegStatsLUT.txt  in the
previous command to the FS folder on your system

The last two commands update aseg.stats and wmparc.stats. They both will
get a new column for SNR values for every roi.


On Fri, Feb 10, 2023 at 10:25 PM MANSON ERIC NAAB 
wrote:

> External Email - Use Caution
>
> Thank you very much for your quick response. I still have a challenge
> locating the output file after running the suggested  command
> ( mri_cnr $SUBJECTS_DIR/bert/surf/ $SUBJECTS_DIR/bert/mri/norm.mgz) with
> my subject.
> Can you please provide me with the full command for calculating
> contrast-to-noise ratio and signal-to-noise ratio of white matter, gray
> matter and CSF since am a beginner Or a video link to calculate them.
>
> This is what i see after running the command
>
> mri_cnr /Applications/freesurfer/7.1.1/SUBNEW/PA1//label/lh.cortex.label
>
> mri_cnr -- compute the gray/white/csf contrast-to-noise ratio for volumes.
>
> usage: mri_cnr [options]...
>
> usage example (assumes fs pipeline has finished for subject subj1):
> mri_cnr subj1/surf subj1/mri/orig.mgz
>
> Available options:
>
> -s : compute slope
> based on given values, write it to slope and offset files labeled
>  (e.g., `lh..slope.mgz')
>
> -t : print only the total CNR to stdout (stderr still contains more
> information)
>
> -l : log cnr to file . Will contain 8 values in the
> following order: gray_white_cnr, gray_csf_cnr, white_mean, gray_mean,
> csf_mean, sqrt(white_var), sqrt(gray_var), sqrt(csf_var)
>
> label  : read hemisphere labels from  and 
>
> -u, -?, -help : print usage information and quit
>
> -version : print software version information and quit.
>
> On Thu, Feb 9, 2023 at 3:46 PM John Anderson  wrote:
>
>> External Email - Use Caution
>>
>> You might consider the command wm-anat-snr to compute SNR
>>
>> On Thu, Feb 9, 2023 at 10:38 AM Kumar, Avnish <
>> avnish.ku...@mgh.harvard.edu> wrote:
>>
>>> You could also use these:
>>>
>>>1. For CNR you can use the mri_cnr tool:
>>>
>>> mri_cnr [options]  
>>>
>>> For example:
>>>
>>> mri_cnr $SUBJECTS_DIR/bert/surf/ $SUBJECTS_DIR/bert/mri/norm.mgz
>>>
>>>
>>>
>>>1. For SNR, you'll have to calculate them as:
>>>   1.
>>>
>>>   Run the recon-all pipeline to process your MRI data.
>>>   2.
>>>
>>>   Use the mri_binarize tool to create a binary mask of the ROI in
>>>   the image.
>>>   3.
>>>
>>>   Use the mri_segstats tool to calculate the mean and standard
>>>   deviation of the intensity values within the ROI.
>>>   4.
>>>
>>>   Then your SNR = mean_intensity/std_of_intensity.
>>>
>>>
>>> Best,
>>>
>>> Avnish
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <
>>> yhuan...@mgh.harvard.edu>
>>> *Sent:* Tuesday, February 7, 2023 9:09 AM
>>> *To:* Freesurfer support list 
>>> *Subject:* Re: [Freesurfer] MRI image quality metrics
>>>
>>>
>>> Hi,
>>>
>>>
>>>
>>> The following is taken from *MailScanner has detected a possible fraud
>>> attempt from "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/15IwpbwQA-WCW8yltQ1qpLfRaQV-8nx8afnQdmUW16GAXDwTUuUE2Uo7ja53lo5m7QrlaFd47dzyShd9KzRS2Es

Re: [Freesurfer] MRI image quality metrics

[John Anderson]

External Email - Use Caution

You might consider the command wm-anat-snr to compute SNR

On Thu, Feb 9, 2023 at 10:38 AM Kumar, Avnish 
wrote:

> You could also use these:
>
>1. For CNR you can use the mri_cnr tool:
>
> mri_cnr [options]  
>
> For example:
>
> mri_cnr $SUBJECTS_DIR/bert/surf/ $SUBJECTS_DIR/bert/mri/norm.mgz
>
>
>
>1. For SNR, you'll have to calculate them as:
>   1.
>
>   Run the recon-all pipeline to process your MRI data.
>   2.
>
>   Use the mri_binarize tool to create a binary mask of the ROI in the
>   image.
>   3.
>
>   Use the mri_segstats tool to calculate the mean and standard
>   deviation of the intensity values within the ROI.
>   4.
>
>   Then your SNR = mean_intensity/std_of_intensity.
>
>
> Best,
>
> Avnish
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <
> yhuan...@mgh.harvard.edu>
> *Sent:* Tuesday, February 7, 2023 9:09 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] MRI image quality metrics
>
>
> Hi,
>
>
>
> The following is taken from
> https://secure-web.cisco.com/1thfo9hWCJUK_nYfNM9axD5kjhrzv1nVC_cWmWT2aic2ttFqLtKhuhi9E6AA5fXRqlBpbp24-HV_sfbVQik2RJDyE7c9eALg8zbpl340Dwhl2aijQIJcCFqj9K_RZhk5xCVRHURT36bgdsm5C36VxQ3fQh7sVLpsmxKo0Ie0hB8HrgI8Rn7JySIK5iCJZWL9q1OqnFWJgdRUgMDrVlJVf356x-vM1sz0IWVGsGErBQNdxLAYcSvFCTWx0fb6tb1mCw7ljDzERXM7qU-fnbvpV-AKWSuj0eVKouZoNRp8SgTUOIA2mR_VbqAJw9K2PU4OKa4g3f30QsCJpd0U1hcNz7Q/https%3A%2F%2Fgithub.com%2FComaRecoveryLab%2FLesion_Correction
>   as mentioned in
> this paper
> https://secure-web.cisco.com/1aMzZKpIcKTLwbYP_79ZqCUH8p9h0Xh4xqpm8fsmVREKN8hATdl6DHCSkFDKqidqmKqoAydr5eDqjVLAQDKN0zmR2k2Wckx-sv1P3JgKJVQWfpIVeyrh0tqwnGzqQm3nK9BQGA7rUSYwaCBBjmogAhlrnepeAo1_J0CQXj4rKMM-V_g9sXIIirV1h-sajPjULI9qcQw2orS-vs9tl65xAbfrEtmtZ35-IZO43Wk-1D2CsVkFyKCsuGxT5qcGTg9FV3VSUbHpeA-dKS1qkv8zYKtz4i-JeRm0y4E6YAs_B91ccue5fFsCAMyN4jKTPxkhNk7f7IRaIrbfA6GYyWFCX7A/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2215016120302144
>
>
>
> “
>
> Qualitative and Quantitative Assessment of MRI Data
>
>
>
> SNR: We calculated SNR for each subject using the “wm-anat-snr” FreeSurfer
> tool available in FreeSurfer v6.0. Voxels from the subject’s normalized T1
> (norm.mgz) that containing white matter (WM) as defined by the subject’s
> aparc+aseg.mgz are used to calculate SNR with this tool.
>
>
>
> SNR = (mean WM)/(stdev WM)
>
>
>
> We ran the following command for each subject:
>
>
>
> wm-anat-snr –s
>
>
>
> CNR: We calculated CNR for each subject using the “mri_cnr” FreeSurfer
> tool available in FreeSurfer v6.0. This tool finds the average between two
> CNRs: the subject’s (1) WM and gray matter (GM) CNR and (2) gray matter and
> cerebrospinal fluid (CSF) CNR. The average CNR is then calculated and
> reported for each hemisphere. Finally, the CNR for both hemispheres are
> averaged to produce a full brain CNR.
>
>
>
> WM-GM CNR = (delta(WM,GM)^2)/(total variance) GM-CSF CNR =
> (delta(GM,CSF)^2)/(total variance) Hemisphere CNR = (WM-GM CNR + GM-CSF
> CNR) x 2 Full Brain CNR = (Left Hemisphere CNR + Right Hemisphere CNR) x 2
>
> “
>
>
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *MANSON ERIC NAAB
> *Sent:* Tuesday, February 7, 2023 5:26 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] MRI image quality metrics
>
>
>
> *External Email - Use Caution*
>
> Dear FreeSurfer experts,
>
> Please, I need your assistance and guidance on calculating the
> contrast-to-noise ratio (CNR) and signal-to-noise-ratio (SNR) of White
> matter, Gray matter, and CSF of the brain after recon-all.
>
>
>
> Thank you
> ___
> Freesurfer mailing list
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> 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 Mass General
> Brigham Compliance HelpLine at
> 

[Freesurfer] change labels name

[John Anderson]

External Email - Use Caution

Dear Freesurfer,
I have a volumetric atlas in nifti format. I can open this atlas in
freeview. Using the Lookup Table>FreesurferColorLUT, I can see how
every label has a specific color. When I move the mouse cursor over an area
of this atlas. I can see the name of that region (label). My question is
how can I edit the name of the regions in that atlas.
I am sorry if my question is basic. I couldn't figure out how to do it :(

Thanks for any advice you may provide.
John
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[Freesurfer] cortocal thickness / gray matter volume

[John Anderson]

External Email - Use Caution

Dear experts,
this is the first time I have used Freesurfer. I am a clinician and I don't
have previous experience. I followed wiki instructions. I have a group of
T1 images. I need cortical thickness and cortical gray matter volume
measurements . I ran "recon-all" and I got all the measurements.
My question is about cortical thickness and cortical gray matter volume,
are these two measurements have to be correlated everytime? Is it possible
to find cases of cortical thinning and normal cortical gray matter volume?
I don't have a solid mathematical background. I am wondering if  those two
numbers must always correlate with each other, otherwise  I am worried that
an error in the analysis may lead to cortical thinning and normal cortical
gray matter volume.

Thank you for your time,
John
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[Freesurfer] mni152reg

[john Anderson]

External Email - Use Caution

Dear FS experts,
I would like to move PET image to MNI152. What is the correct command to do so. 
I tried
mri_vol2vol --mov PET.nii.gz --s subjID --targ 
$SUBJECTS_DIR/subjID/mri/orig.mga --regheader --o PET_T1.nii.gz

mni152reg --s subjID
then
mri_vol2vol --inv --targ PET_T1.nii.gz --mov 
$FSL_DIR/data/standard/MNI152_T1_2mm_brain.nii.gz --o PET_T1_2MNI153_2mm.nii.gz 
--interp nearest --reg $SUBJECTS_DIR/subjID/mri/transforms/reg.mni152.reg.dat

I still not happy with thresults. PET not perfectly moved to MNI.
please are the steps above correct? Can you kindly suggest any ideas to improve 
PET registration to MNI?

Thanks
John___
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Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

[john Anderson]

External Email - Use Caution

Hi Dr Greve,

Yes, in my lab we normalize DPA713 tracer to whole brain mean using the command 
fslmaths something like
fslmaths pet.nii -mask mask  -inm 1 pet_normalized_whole_brain.nii.gz

For kinetic modeling.. kindly I would like to be sure that I got it right.
I am doing kinetic modeling for two groups of subjects patients and controls.
I am following PET surfer tutorial. In the case of patients and healthy 
controls comparison I can use MRTM1 and MRTM2 correct?

Also for the flag "--km-hb" are the IDs that I need to feed to this flag 
represent regions of high binding affinity in patients or healthy controls or 
it doesn't matter just regions known to have high binding. For example some 
tracers show regions of high binding affinity on healthy scans as well as 
patients scans.

On 2/22/19 11:43 AM, john Anderson wrote:

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Dear Dr Greve,

Thank you so much for the response! Indeed, I used MRTM2 for HB pathological 
regions and the results were very confusing Based on your response bellow, 
I understand that for pathological regions I can feed "bp.nii.gz" files from 
"MRTM1" not "MRTM2" to a surface based analyses. Is this correct?

You can actually use either MRTM1 or MRTM2 for further analysis, but I think 
the way I have it documented, you would use MRTM2.

Also for the flag "--km-ref", I have interest in doing whole brain 
normalization (i.e. all ROIs in wmparc.mgz) in this case do I need to feed all 
the numbers relevant to all ROIs in gtmseg.ctab. Is there any way to let 
--km-ref know that I want to do whole brain normalization without feeding a 
very long list of numbers?

No, I don't think so. Sorry, I never considered this case. Are you sure that is 
what you want to do?

Thank you so much for help

John

On 2/22/19 7:58 AM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,

I would like to use petsurfet to do kinetic modeling (KM), the pipeline is 
straightforward and easy to use. Thank you so much! I would appreciate any 
clarifications relevant to my questions bellow:

1) I understand that the flag "--km-ref" define the reference region for 
normalizing PET signal. in the linear below the reference region is cerebellum 
cortex. If we need to normalize to occipital just we change the numbers based 
on labels in aparc+aseg atlas?

Yes.

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale

2) --km-hb define the high binding regions. Are these regions represent the 
regions that are pathologically involved where we expect it to have higher PET 
signal OR it represent the regions where PET tracer has the maximum binding in 
general regardless of pathology? I mean every tracer have high level in 
specific regions in the brain is this what the flag is referring too?

I have not dealt with pathological cases with MRTM2. I would avoid using them 
for the HB region as their kinetics may be different than healthy tissue.

Thanks for any clarification,

John

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Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

[john Anderson]

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Dear Dr Greve,

Thank you so much for the response! Indeed, I used MRTM2 for HB pathological 
regions and the results were very confusing Based on your response bellow, 
I understand that for pathological regions I can feed "bp.nii.gz" files from 
"MRTM1" not "MRTM2" to a surface based analyses. Is this correct?

Also for the flag "--km-ref", I have interest in doing whole brain 
normalization (i.e. all ROIs in wmparc.mgz) in this case do I need to feed all 
the numbers relevant to all ROIs in gtmseg.ctab. Is there any way to let 
--km-ref know that I want to do whole brain normalization without feeding a 
very long list of numbers?

Thank you so much for help
John

On 2/22/19 7:58 AM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,

I would like to use petsurfet to do kinetic modeling (KM), the pipeline is 
straightforward and easy to use. Thank you so much! I would appreciate any 
clarifications relevant to my questions bellow:

1) I understand that the flag "--km-ref" define the reference region for 
normalizing PET signal. in the linear below the reference region is cerebellum 
cortex. If we need to normalize to occipital just we change the numbers based 
on labels in aparc+aseg atlas?

Yes.

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale

2) --km-hb define the high binding regions. Are these regions represent the 
regions that are pathologically involved where we expect it to have higher PET 
signal OR it represent the regions where PET tracer has the maximum binding in 
general regardless of pathology? I mean every tracer have high level in 
specific regions in the brain is this what the flag is referring too?

I have not dealt with pathological cases with MRTM2. I would avoid using them 
for the HB region as their kinetics may be different than healthy tissue.

Thanks for any clarification,

John___
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[Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

[john Anderson]

External Email - Use Caution

Hi Dr Greve,
I would like to use petsurfet to do kinetic modeling (KM), the pipeline is 
straightforward and easy to use. Thank you so much! I would appreciate any 
clarifications relevant to my questions bellow:
1) I understand that the flag "--km-ref" define the reference region for 
normalizing PET signal. in the linear below the reference region is cerebellum 
cortex. If we need to normalize to occipital just we change the numbers based 
on labels in aparc+aseg atlas?

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale

2) --km-hb define the high binding regions. Are these regions represent the 
regions that are pathologically involved where we expect it to have higher PET 
signal OR it represent the regions where PET tracer has the maximum binding in 
general regardless of pathology? I mean every tracer have high level in 
specific regions in the brain is this what the flag is referring too?

Thanks for any clarification,
John___
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Re: [Freesurfer] mri_convert

[john Anderson]

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Hi Dr Greve,

Thanks for the response.
yes, I need to extract the acquisition times for kinetic modeling using PET 
surfer. Please I have two follow-up questions and I appreciate any highlights:
- Are the acquisition times that PET surfer needs to be included in a file 
called time.dat can be extracted from the PET DICOM header - tag (0008 ,0013) 
which labeled "Instance Creation Time" is this the correct tag?
- intensity scaling is not imbedded in the dicom, do you kindly suggest how I 
can convert the PET DICOMS to nifti?

Thanks so much!
John

you mean you want the acquisition times to do kinetic modeling? I don't have 
anything to do that. Also, you should check to see whether your PET has 
intensity scaling imbedded in the dicom as the v6 mri_convert does not handle 
this properly.

On 2/20/19 11:44 AM, john Anderson wrote:

>

> External Email - Use Caution

>

> hi FS experts.

> I would like to inquire about the command mri_ convert I use this

> command to convert fMRI and PET 4D volumes from dicom format to nifti.

>

> Are there any flags that can be used in mri_convert command line to

> enable it to extract a text file contain each series time in seconds?

>

> thanks

> John

>

>

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[Freesurfer] mri_convert

[john Anderson]

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hi FS experts.
I would like to inquire about the command mri_ convert
I use this command to convert fMRI and PET 4D volumes from dicom format to 
nifti.

Are there any flags that can be used in mri_convert command line to enable it 
to extract a text file contain each series time in seconds?

thanks
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[Freesurfer] dtrecon

[john Anderson]

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Hi FS experts,
I would like to inquire about the command "dtrecon" in Freesurfer.
Is this command able to process multishell diffusion data? if not would you 
recommend any method?

Thanks in advance
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Re: [Freesurfer] move statistical map onto the cerebellum surface

[john Anderson]

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Hi Dr Greve, yes  indeed I used the flag "projfrac" and I missed including it 
in my command bellow. I greatly apologize!

My I kindly ask, if "projfrac" is not used then at which layer of the 
cerebellum the projection will take place, is it 0.5? Also, is there any method 
that can help to use "projfrac".
I apologies if my questions are overwhelming. I am just trying to learn how to 
it correctly. Thanks

It should only do that if you have specified a projection fraction. Is that 
your full command line? Can you send the full terminal output?

On 1/24/19 4:56 PM, john Anderson wrote:

>

> External Email - Use Caution

>

> Hi Dr Greve, I appreciate your guidance very much.

>

> I followed your suggestion. I put lh.cerebellum in fsaverage and I ran

> mri_vol2surf.

> as follows:

> mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf

> cerebellum --mni152reg --o grf_onto_cerebellum.nii.gz

>

> Now I am getting this error

>

> ERROR: number of vertices in /FSV6.0/fsaverage/surf/lh.thickness does

> not match surface (163842,34247)

>

> Any suggestions are appreciated ;-)

> John

> ‐‐‐ Original Message ‐‐‐

On Thursday, January 24, 2019 4:56 PM, john Anderson 
 wrote:

> Hi Dr Greve, I appreciate your guidance very much.
>
> I followed your suggestion. I put lh.cerebellum in fsaverage and I ran 
> mri_vol2surf.
> as follows:
> mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf cerebellum 
> --mni152reg --o grf_onto_cerebellum.nii.gz
>
> Now I am getting this error
>
> ERROR: number of vertices in /FSV6.0/fsaverage/surf/lh.thickness does not 
> match surface (163842,34247)
>
> Any suggestions are appreciated ;-)
> John
>
> You will have to put the cerebellar surface in fsaverage/surf/lh.cerebellum 
> Note use "lh" even if it is the entire cerebellum as FS commands generally 
> require a hemisphere.
>
> The run mri_vol2surf specifying --hemi lh --surf cerebellum
>
> On 1/23/19 10:04 AM, john Anderson wrote:
>
>>
>
>> External Email - Use Caution
>
>>
>
>> Dear FS experts,
>
>> I ran surface based PET analysis on subcortical regions. Then
>
>> corrected the results for multiple comparisons using  the method --grf
>
>> in the command mri_glmfit-sim.
>
>>
>
>> I can visualize the output of multiple comparisons (i.e. the file
>
>> grf.th1.3.pos.sig.cluster.mgh) on volume using tkmedit, this
>
>> statistical map shows difference between the groups in the
>
>> cerebellum Instead of visualizing the results on volume, I want to
>
>> move this file to the cerebellum surface. I already created the
>
>> cerebellum surfaces from aseg.mgz file in fsaverage using the command
>
>> mris_tesselate.
>
>>
>
>> How can I move the the file grf.th1.3.pos.sig.cluster.mgh from volume
>
>> space and map it on the cerebellum surface?
>
>>
>
>> I tried mri_vol2surf but this command requires the flag --hemi as a
>
>> result it will map the file "grf.th1.3.pos.sig.cluster.mgh" on
>
>> cerebral hemispheres (lh or rh) but not the cerebellum..
>
>> How can I map the file "grf.th1.3.pos.sig.cluster.mgh" on the
>
>> cerebellum surface?
>
>>
>
>> Thanks for any suggestions,
>
>> John
>
>>
>
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>
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>
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>
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>
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Re: [Freesurfer] move statistical map onto the cerebellum surface

[john Anderson]

External Email - Use Caution

Hi Dr Greve, I appreciate your guidance very much.

I followed your suggestion. I put lh.cerebellum in fsaverage and I ran 
mri_vol2surf.
as follows:
mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf cerebellum 
--mni152reg --o grf_onto_cerebellum.nii.gz

Now I am getting this error

ERROR: number of vertices in /FSV6.0/fsaverage/surf/lh.thickness does not match 
surface (163842,34247)

Any suggestions are appreciated ;-)
John

You will have to put the cerebellar surface in fsaverage/surf/lh.cerebellum 
Note use "lh" even if it is the entire cerebellum as FS commands generally 
require a hemisphere.

The run mri_vol2surf specifying --hemi lh --surf cerebellum

On 1/23/19 10:04 AM, john Anderson wrote:

>

> External Email - Use Caution

>

> Dear FS experts,

> I ran surface based PET analysis on subcortical regions. Then

> corrected the results for multiple comparisons using  the method --grf

> in the command mri_glmfit-sim.

>

> I can visualize the output of multiple comparisons (i.e. the file

> grf.th1.3.pos.sig.cluster.mgh) on volume using tkmedit, this

> statistical map shows difference between the groups in the

> cerebellum Instead of visualizing the results on volume, I want to

> move this file to the cerebellum surface. I already created the

> cerebellum surfaces from aseg.mgz file in fsaverage using the command

> mris_tesselate.

>

> How can I move the the file grf.th1.3.pos.sig.cluster.mgh from volume

> space and map it on the cerebellum surface?

>

> I tried mri_vol2surf but this command requires the flag --hemi as a

> result it will map the file "grf.th1.3.pos.sig.cluster.mgh" on

> cerebral hemispheres (lh or rh) but not the cerebellum..

> How can I map the file "grf.th1.3.pos.sig.cluster.mgh" on the

> cerebellum surface?

>

> Thanks for any suggestions,

> John

>

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[Freesurfer] move statistical map onto the cerebellum surface

[john Anderson]

External Email - Use Caution

Dear FS experts,
I ran surface based PET analysis on subcortical regions. Then corrected the 
results for multiple comparisons using  the method --grf in the command 
mri_glmfit-sim.

I can visualize the output of multiple comparisons (i.e. the file 
grf.th1.3.pos.sig.cluster.mgh) on volume using tkmedit, this statistical map 
shows difference between the groups in the cerebellum Instead of 
visualizing the results on volume, I want to move this file to the cerebellum 
surface. I already created the cerebellum surfaces from aseg.mgz file in 
fsaverage using the command mris_tesselate.

How can I move the the file grf.th1.3.pos.sig.cluster.mgh from volume space and 
map it on the cerebellum surface?

I tried mri_vol2surf but this command requires the flag --hemi as a result it 
will map the file "grf.th1.3.pos.sig.cluster.mgh" on cerebral hemispheres (lh 
or rh) but not the cerebellum..
How can I map the file "grf.th1.3.pos.sig.cluster.mgh" on the cerebellum 
surface?

Thanks for any suggestions,
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[Freesurfer] correction for multiple comparison: simulation vs grf vs cache

[john Anderson]

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Hi Dr Greve,
I would like to correct surface based analyses of PET data for multiple 
comparisons. I ran group comparisons in three spaces. left and right 
hemispheres and subcortical.
I used the method --cache in mri_glmfit-sim to correct the analyses in eft and 
right hemispheres.
I used the method --grf in mri_glmfit-sim to correct the analyses in 
subcortical regions.
My questions are:

In one of your kind responses to a collegue here 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-January/035650.html
you had suggested  "If you want to use GRF, you should use smooth by twice the 
native voxel size. I would not go higher than .01 on the threshold".
Would you mind clarify what it means don;t go higher than .01 is this the cwp 
threshold? also smoothing by twice the native voxel is this means fwhm=2mm?

The methods --cache and --grf are giving me the expected results.. when  I 
should consider using simulation --perm ?

Thanks for any clarification
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Re: [Freesurfer] mapping a volumetric statistical map to the cerebellum surface

[john Anderson]

External Email - Use Caution

Hi Dr Greve,

Thanks for the comment:
I ran vertex wise analysis on subcortical regions, I corrected the analysis for 
multiple comparison using "mri_glmfit-sim". One of the created files after 
correction for multiple comparison is "grf.th1.3.pos.sig.cluster.mgh"
I would like to move this file to the cerebellum surface? I used the command

mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf white 
--projfrac 0 --mni152reg --o lh.grf.th1.3.pos.sig.cluster.mgh

I want to project "grf.th1.3.pos.sig.cluster.mgh" on the cerebellum surface (I 
already created surfaces to the cerebellum using the command mri_tesselate), 
but it seems that he command mri_vol2surf is designed to move files to the 
cerebral surfaces not to the cerebellum surfaces. How can I modify the command 
to project statistical maps on specific structural surfaces such as cerebellum 
and brain stem?

Thanks
John

Can you be more specific about how mri_vol2surf failed? Eg, command line, 
terminal output, reason you think it did not work

On 1/21/19 10:47 AM, john Anderson wrote:

>

> External Email - Use Caution

>

> Dear FS experts,

> I have a statistical map from the output of a surface based analysis

> in subcortical regions. This statistical map shows significant

> difference between the groups in the cerebellum cortex.

>

> I reconstructed the cerebellar surfaces using the command

> "mri_tessalte). Now, I would like to map the volumetric statistical

> map to the constructed cerebellum surfaces. How can I do that? I tried

> the command "mri_vol2surf" in many different wants but it didn't work!

>

> Thanks for any guidance!

> John
‐‐‐ Original Message ‐‐‐
On Monday, January 21, 2019 10:47 AM, john Anderson 
 wrote:

> Dear FS experts,
> I have a statistical map from the output of a surface based analysis in 
> subcortical regions. This statistical map shows significant difference 
> between the groups in the cerebellum cortex.
>
> I reconstructed the cerebellar surfaces using the command "mri_tessalte). 
> Now, I would like to map the volumetric statistical map to the constructed 
> cerebellum surfaces. How can I do that? I tried the command "mri_vol2surf" in 
> many different wants but it didn't work!
>
> Thanks for any guidance!
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Re: [Freesurfer] fsaverage, brainstem and cerebellum

[john Anderson]

External Email - Use Caution

Hi Dr Greve, thank you for the response... It is a genius hack ;-)
Results are way much better. My objective is just to improve visualization...
I would like to project statistical maps from vertex wise analysis of 
subcortical regions.

The same last figure in FSFAST Freesurfer WIKI

https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel

But instead of visualizing the merged statistical map of the three spaces on 
volume, I would like to project it on surface. I have results in the cerebellum 
and brain stem and I want to show it on surface not volume

Also, it Would be appreciated if you provide any suggestions for a 
brain+cerebellum+brain stem template that can be used instead of fsaverage ...

Thank you so much!
John


You can try mri_binarize with both --erode and --dilate (specifying the 
structures with --match and and output surface with --surf). Dilating then 
eroding might remove some of the holes (though it is a hack)




On 1/22/19 10:43 AM, Bruce Fischl wrote:
> Hi John
>
> sorry, not really. If you constrain the topology of the cerebellum you
> will probably loose a lot of it since the folia are so small. You can
> try using Florent Segonne's old code (mri_topologycorrection), which
> will generate a discrete segmentation that has the correct topology
> (hopefully!), but I don't believe that guarantees that covering the
> surface of it will also be topologically correct.
>
> cheers
> Bruce
>
>
> On Tue, 22 Jan 2019, john Anderson wrote:


‐‐‐ Original Message ‐‐‐
On Tuesday, January 22, 2019 7:36 AM, john Anderson 
 wrote:

> Hi Dr Bruce,
> I applied your recommendations and I was able to create surfaces to the 
> cerebellum and brain stem using the command mri_tesselate. I am not happy 
> with the topology though... There are holes and some defects. Would you 
> recommend any commands to improve the topology of these structures?
> Your guidance is appreciated,
> John
>
> Sent with ProtonMail Secure Email.
>
> ‐‐‐‐‐‐‐ Original Message ‐‐‐
> On Thursday, January 10, 2019 1:37 PM, john Anderson 
> john.ande...@protonmail.com wrote:
>
> > Ah! great!! thank you so much for the great help!!
> > Have a good day,
> > John
> > Sent with ProtonMail Secure Email.
> > ‐‐‐ Original Message ‐‐‐
> > On Thursday, January 10, 2019 1:03 PM, Bruce Fischl 
> > fis...@nmr.mgh.harvard.edu wrote:
> >
> > > Hi John
> > > we distribute an aseg.mgs with fsaverage I believe. You can just
> > > tesselate that.
> > > cheers
> > > Bruce
> > > On Thu, 10 Jan 2019, john Anderson wrote:
> > >
> > > > External Email - Use Caution
> > > > Hi Dr Bruce, I highly appreciate your guidance.
> > > > I would like to load the cerebellum and brain stem structures as an 
> > > > average structure similar to
> > > > "fsaverage" , I usually use the command
> > > > tksurferfv fsaverage lh pial -overlay 
> > > > mri_tessellate or mri_mc would create a surface for every subject, how 
> > > > can I create the average of the
> > > > surfaces of those structures similar to "fsaverage"?
> > > > Thanks again for any highlights
> > > > John
> > > > Hi John
> > > > you could use mri_tessellate or mri_mc to create a surface for those 
> > > > structures, then smooth them with
> > > > mris_smooth and load them into freeview.
> > > > Shouldn't be too hard.
> > > > cheers
> > > > Bruce
> > > > On Thu, 10 Jan 2019, john Anderson
> > > > wrote:
> > > > ‐‐‐ Original Message ‐‐‐
> > > > On Thursday, January 10, 2019 7:40 AM, john Anderson 
> > > > john.ande...@protonmail.com wrote:
> > > >
> > > >   Dear FS experts,
> > > >
> > > >
> > > > For visualization purposes, is there any way to show the cerebellum and 
> > > > brain stem regions
> > > > (similar to the attached figure), this figure was published used CONN 
> > > > toolbox but I am not sure
> > > > how they were able to map functional data in brain surface and show the 
> > > > cerebellum and brain
> > > > stem with fsaverage.
> > > > I appreciate any suggestion
> > > > Jon



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Re: [Freesurfer] fsaverage, brainstem and cerebellum

[john Anderson]

External Email - Use Caution

Hi Dr Bruce,
I applied your recommendations and I was able to create surfaces to the 
cerebellum and brain stem using the command mri_tesselate. I am not happy with 
the topology though... There are holes and some defects. Would you recommend 
any commands to improve the topology of these structures?
Your guidance is appreciated,
John


Sent with ProtonMail Secure Email.

‐‐‐ Original Message ‐‐‐
On Thursday, January 10, 2019 1:37 PM, john Anderson 
 wrote:

> Ah! great!! thank you so much for the great help!!
> Have a good day,
> John
>
> Sent with ProtonMail Secure Email.
>
> ‐‐‐ Original Message ‐‐‐
> On Thursday, January 10, 2019 1:03 PM, Bruce Fischl 
> fis...@nmr.mgh.harvard.edu wrote:
>
> > Hi John
> > we distribute an aseg.mgs with fsaverage I believe. You can just
> > tesselate that.
> > cheers
> > Bruce
> > On Thu, 10 Jan 2019, john Anderson wrote:
> >
> > > External Email - Use Caution
> > > Hi Dr Bruce, I highly appreciate your guidance.
> > > I would like to load the cerebellum and brain stem structures as an 
> > > average structure similar to
> > > "fsaverage" , I usually use the command
> > > tksurferfv fsaverage lh pial -overlay 
> > > mri_tessellate or mri_mc would create a surface for every subject, how 
> > > can I create the average of the
> > > surfaces of those structures similar to "fsaverage"?
> > > Thanks again for any highlights
> > > John
> > > Hi John
> > > you could use mri_tessellate or mri_mc to create a surface for those 
> > > structures, then smooth them with
> > > mris_smooth and load them into freeview.
> > > Shouldn't be too hard.
> > > cheers
> > > Bruce
> > > On Thu, 10 Jan 2019, john Anderson
> > > wrote:
> > > ‐‐‐ Original Message ‐‐‐
> > > On Thursday, January 10, 2019 7:40 AM, john Anderson 
> > > john.ande...@protonmail.com wrote:
> > >
> > >   Dear FS experts,
> > >
> > >
> > > For visualization purposes, is there any way to show the cerebellum and 
> > > brain stem regions
> > > (similar to the attached figure), this figure was published used CONN 
> > > toolbox but I am not sure
> > > how they were able to map functional data in brain surface and show the 
> > > cerebellum and brain
> > > stem with fsaverage.
> > > I appreciate any suggestion
> > > Jon



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[Freesurfer] mapping a volumetric statistical map to the cerebellum surface

[john Anderson]

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Dear FS experts,
I have a statistical map from the output of a surface based analysis in 
subcortical regions. This statistical map shows significant difference between 
the groups in the cerebellum cortex.

I reconstructed the cerebellar surfaces using the command "mri_tessalte). Now, 
I would like to map the volumetric statistical map to the constructed 
cerebellum surfaces. How can I do that? I tried the command "mri_vol2surf" in 
many different wants but it didn't work!

Thanks for any guidance!
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[Freesurfer] Average of surfaces

[john Anderson]

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Dear FS experts,
I resampled PET images for multiple subjects I used mri_vol2surfe to move these 
images onto fsaverage, not I have for every subject lh.PET and rh.PET

How can I create the average of multiple surfaces. For example:
on the left hemisphere of every subject I have
lh.PET.subject1.nii,gz, lh.PET.subject2.nii,gz, lh.PET.subject3.nii,gz,  
lh.PET.subjectN.nii,gz

How can I create the average of these surfaces?
Thanks for any help
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Re: [Freesurfer] fsaverage, brainstem and cerebellum

[john Anderson]

External Email - Use Caution

Ah! great!! thank you so much for the great help!!
Have a good day,
John


Sent with ProtonMail Secure Email.

‐‐‐ Original Message ‐‐‐
On Thursday, January 10, 2019 1:03 PM, Bruce Fischl 
 wrote:

> Hi John
>
> we distribute an aseg.mgs with fsaverage I believe. You can just
> tesselate that.
>
> cheers
> Bruce
> On Thu, 10 Jan 2019, john Anderson wrote:
>
> > External Email - Use Caution
> > Hi Dr Bruce, I highly appreciate your guidance.
> > I would like to load the cerebellum and brain stem structures as an average 
> > structure similar to
> > "fsaverage" , I usually use the command
> > tksurferfv fsaverage lh pial -overlay 
> > mri_tessellate or mri_mc would create a surface for every subject, how can 
> > I create the average of the
> > surfaces of those structures similar to "fsaverage"?
> > Thanks again for any highlights
> > John
> > Hi John
> >
> > you could use mri_tessellate or mri_mc to create a surface for those 
> > structures, then smooth them with
> > mris_smooth and load them into freeview.
> > Shouldn't be too hard.
> >
> > cheers
> > Bruce
> >
> > On Thu, 10 Jan 2019, john Anderson
> > wrote:
> > ‐‐‐ Original Message ‐‐‐
> > On Thursday, January 10, 2019 7:40 AM, john Anderson 
> > john.ande...@protonmail.com wrote:
> >
> >   Dear FS experts,
> >
> >
> > For visualization purposes, is there any way to show the cerebellum and 
> > brain stem regions
> > (similar to the attached figure), this figure was published used CONN 
> > toolbox but I am not sure
> > how they were able to map functional data in brain surface and show the 
> > cerebellum and brain
> > stem with fsaverage.
> > I appreciate any suggestion
> > Jon



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Re: [Freesurfer] fsaverage, brainstem and cerebellum

[john Anderson]

External Email - Use Caution

Hi Dr Bruce, I highly appreciate your guidance.
I would like to load the cerebellum and brain stem structures as an average 
structure similar to "fsaverage" , I usually use the command

tksurferfv fsaverage lh pial -overlay 

mri_tessellate or mri_mc would create a surface for every subject, how can I 
create the average of the surfaces of those structures similar to "fsaverage"?

Thanks again for any highlights
John

Hi John

you could use mri_tessellate or mri_mc to create a surface for those 
structures, then smooth them with mris_smooth and load them into freeview.

Shouldn't be too hard.

cheers

Bruce

On Thu, 10 Jan 2019, john Anderson

wrote:

‐‐‐ Original Message ‐‐‐
On Thursday, January 10, 2019 7:40 AM, john Anderson 
 wrote:

> Dear FS experts,
> For visualization purposes, is there any way to show the cerebellum and brain 
> stem regions (similar to the attached figure), this figure was published used 
> CONN toolbox but I am not sure how they were able to map functional data in 
> brain surface and show the cerebellum and brain stem with fsaverage.
> I appreciate any suggestion
> Jon___
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[Freesurfer] fsaverage, brainstem and cerebellum

[john Anderson]

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Dear FS experts,
For visualization purposes, is there any way to show the cerebellum and brain 
stem regions (similar to the attached figure), this figure was published used 
CONN toolbox but I am not sure how they were able to map functional data in 
brain surface and show the cerebellum and brain stem with fsaverage.
I appreciate any suggestion
Jon___
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[Freesurfer] Surface based analysis - circular analysis?

[john Anderson]

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Dear experts,
I have three groups:
- pre treatment (baseline)
- post treatment (follow-up after 6 month of the baseline visit)
- healthy controls.

The three groups have PET data. I ran surface based paired t test  between pre 
and post treatment. The analysis failed to show significant change in the 
signal between baseline and follow-up visits. As an alternative approach I 
tried:
- Surface-based analysis between pre treatment vs healthy controls. This 
analysis found cluster A of significant difference
- Surface-based analysis between post treatment vs healthy controls. This 
analysis found cluster B of significant difference

I subtracted the two clusters A and B then I used the resultant mask (the 
difference between the clusters A and B) to measure the required signal.

Colleague of mine said that this might be criticized for being circular and it 
may not be acceptable? My understanding is that this analysis is not circular 
because the signal was measured in a completely new region represents the 
difference between two clusters.

I appreciate any suggestion or highlights!

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[Freesurfer] Fw: Surface based paired t test

[john Anderson]

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Hi Dr Greve, yes exactly this is what I did. i user mri_corg and I got the 
reg.lta file. Then I used mris_preproc with the flag --iv but this output an 
error message that the flags --fsgd, paired-diff and --iv doesn't work 
together. This is the reason for my question.

I appreciate any suggestion.

If you have not sampled the PET data onto the surface, you will need to run 
mri_coreg to create a registration to the anatomical. Then use can use 
mris_preproc with the --iv option (listing each subject with a different --iv). 
Run mris_preproc with --help to get examples

On 12/06/2018 12:31 PM, john Anderson wrote:

>

> External Email - Use Caution

>

> Hi Dr Greve,

>> I tried to follow this web page

>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis

>> This tutorial seems to be for cortical thickness data. After sampling

>> each individual's surface onto the average surface, how can I modify

>> this command to fit PET data mris_preproc --target fsaverage --hemi

>> lh \

>> --meas thickness --out lh.paired-diff.thickness.mgh \

>> --fsgd pairs.fsgd --paired-diff

>>

>>

>> Thanks for any help!

>> John

>>

>>

>> ‐‐‐ Original Message ‐‐‐

>> On Tuesday, November 20, 2018 6:34 PM, john Anderson

>>  wrote:

>>

>>> Dear Freesurfer experts,

>>> I would like to run surface based paired  t test of PET data on

>>> surface. For every subject I have visit pre treatment and post

>>> treatment. I tried to follow the instructions here

>>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the

>>> toturial seems to be for cortical thickness data.

>>> How can i modify the command mris_preproc to do paired test of PEt

>>> data on brain surface

>>>   mris_preproc --target fsaverage --hemi lh \

>>> --meas thickness --out lh.paired-diff.thickness.mgh \

>>> --fsgd pairs.fsgd --paired-diff

>>> thanks for any suggestion

>>> John

>>

>

>

>

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[Freesurfer] Surface based paired t test

[john Anderson]

External Email - Use Caution

Hi Dr Greve,

> I tried to follow this web page 
> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> This tutorial seems to be for cortical thickness data. After sampling each 
> individual's surface onto the average surface, how can I modify this command 
> to fit PET data
>
> mris_preproc --target fsaverage --hemi lh \
>--meas thickness --out lh.paired-diff.thickness.mgh \
>--fsgd pairs.fsgd --paired-diff
>
> Thanks for any help!
> John
>
> ‐‐‐ Original Message ‐‐‐
> On Tuesday, November 20, 2018 6:34 PM, john Anderson 
>  wrote:
>
>> Dear Freesurfer experts,
>> I would like to run surface based paired  t test of PET data on surface. For 
>> every subject I have visit pre treatment and post treatment. I tried to 
>> follow the instructions here 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the toturial 
>> seems to be for cortical thickness data.
>> How can i modify the command mris_preproc to do paired test of PEt data on 
>> brain surface
>>
>> mris_preproc --target fsaverage --hemi lh \
>>--meas thickness --out lh.paired-diff.thickness.mgh \
>>--fsgd pairs.fsgd --paired-diff
>>
>> thanks for any suggestion
>> John___
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Re: [Freesurfer] Surface based paired t test

[john Anderson]

External Email - Use Caution

Hi Dr Greve,
I tried to follow this web page 
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
This tutorial seems to be for cortical thickness data. After sampling each 
individual's surface onto the average surface, how can I modify this command to 
fit PET data

mris_preproc --target fsaverage --hemi lh \
   --meas thickness --out lh.paired-diff.thickness.mgh \
   --fsgd pairs.fsgd --paired-diff

Thanks for any help!
John

‐‐‐ Original Message ‐‐‐
On Tuesday, November 20, 2018 6:34 PM, john Anderson 
 wrote:

> Dear Freesurfer experts,
> I would like to run surface based paired  t test of PET data on surface. For 
> every subject I have visit pre treatment and post treatment. I tried to 
> follow the instructions here 
> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the toturial 
> seems to be for cortical thickness data.
> How can i modify the command mris_preproc to do paired test of PEt data on 
> brain surface
>
> mris_preproc --target fsaverage --hemi lh \
>--meas thickness --out lh.paired-diff.thickness.mgh \
>--fsgd pairs.fsgd --paired-diff
>
> thanks for any suggestion
> John___
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[Freesurfer] average of surfaces

[john Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I have multiple PET volumetric images in MNI standard space. I can average (or 
get the Tmean) of these images using fslmerge then fslmaths. I would like to do 
something similar on surfaces images.
I registered the images from native space to Freesurfer space using spmregister 
as follows:
spmregister ---s $subject -mov PET.nii.gz --reg reg.dat --o PET_T1.mgh

Then I used mris_preproc with the flag --mean to register the volumetric images 
to fsaverage, then concatenate the surfaces and average it as follows:
mris_preproc --target fsaverage --hemi lh --projfrac 0.5 --iv PET_T1_subj1 
reg_subj1.dat --iv PET_T1_subj2 reg_subj2.dat . .. .--iv PET_T1_subjN 
reg_subjN.dat --mean --o lh.mgh

the final output "lh.mgh" is an empty image. I am not sure what I am doing 
wrong here.
Any guidance to average the surfaces images in fsaverage would be highly 
appreciated.

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[Freesurfer] Surface based paired t test

[john Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I would like to run surface based paired  t test of PET data on surface. For 
every subject I have visit pre treatment and post treatment. I tried to follow 
the instructions here https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis 
but the toturial seems to be for cortical thickness data.
How can i modify the command mris_preproc to do paired test of PEt data on 
brain surface

mris_preproc --target fsaverage --hemi lh \
   --meas thickness --out lh.paired-diff.thickness.mgh \
   --fsgd pairs.fsgd --paired-diff

thanks for any suggestion
John___
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[Freesurfer] Map image in MNI onto fsaverage

[john Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I have the mean PET images for a number of subjects in MNI152 space. For 
visualization purposes, I would like to map this mean image onto brain surface. 
How can I do it. I appreciate any suggestion you may provide.
Thanks!
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Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics between groups analyses

[John Anderson]

External Email - Use Caution

Dear Dr Greve and Matt, your valable responses and explanations are highly 
appreciated!! Thank you so much!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Sunday, August 5, 2018 6:01 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics 
between groups analyses

If you have only two protocols “high quality” and “low quality", you could 
presumably include a protocol variable as a covariate of no interest, thereby 
removing any effects that correlate with protocol.  For this to work ideally, 
you would have similar numbers of low and high quality protocols across your 
comparison groups.  I agree with Doug that SNR will generally tend to make 
results more variable, but not necessarily in a specific direction.

Matt.
From:  on behalf of Douglas Greve 

Reply-To: Freesurfer support list 
Date: Sunday, August 5, 2018 at 4:48 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics 
between groups analyses

I thought I answered this question last week. See my rsponse below

I don't think it is correct conceptually.  By including SNR as a covariate, you 
are saying that you expect the thickness to increase with higher SNR and 
decrease with lower SNR. This does not make sense to me. It sounds like you are 
trying to do a mixed effects analysis where you weight by the SNR. Still, 
mathematically, this is not a true mixed effect analysis (which requires 
estimates of the within and between subject noise). `

On 8/3/18 10:57 AM, John Anderson wrote:

‐‐‐ Original Message ‐‐‐
On August 5, 2018 1:04 PM, John Anderson  wrote:

>> Dear FS experts,
>> I would like to inquire about including SNR as a covariate for the between 
>> groups comparison in cortical thickness. Is this procedure valid? I have 
>> some T1 images of low quality and the majority are high in quality. I 
>> reviewed the segmentation and the cortical surfaces and fixed manually as 
>> possible. I don't want to exclude images from the data sets, so I am 
>> thinking of regressing out SNR.
>> It seems that the command "mri_segstats" can report SNR for every ROI in the 
>> brain. Is it correct to include whole brain SNR covariate for between group 
>> comparisons (cortical thickness and volumetric analyses).
>> If yes, do I need to include actual SNR values in the FSGD file or the 
>> demeaned values ?
>>
>> We appreciate your guidance!
>> John___
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Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics between groups analyses

[John Anderson]

External Email - Use Caution

> Dear FS experts,
> I would like to inquire about including SNR as a covariate for the between 
> groups comparison in cortical thickness. Is this procedure valid? I have some 
> T1 images of low quality and the majority are high in quality. I reviewed the 
> segmentation and the cortical surfaces and fixed manually as possible. I 
> don't want to exclude images from the data sets, so I am thinking of 
> regressing out SNR.
> It seems that the command "mri_segstats" can report SNR for every ROI in the 
> brain. Is it correct to include whole brain SNR covariate for between group 
> comparisons (cortical thickness and volumetric analyses).
> If yes, do I need to include actual SNR values in the FSGD file or the 
> demeaned values ?
>
> We appreciate your guidance!
> John___
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[Freesurfer] SNA covariate in cortical thickness between groups analysis

[John Anderson]

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Daer FS experts,
I would like to inquire about including SNR as a covariate for the between 
groups cpmparison in cortical thickness. Is this procedure correct 
mathematically? Do I need to demean the SNA values before including it 
covariates? Finally, do you recommend any quality parameters other than SNR to 
be included covariate?

I look forward to learn from your expertise,
Thanks,
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Re: [Freesurfer] Filling holes

[John Anderson]

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Dear Dr Bruce, thank you!!

Hi John

you can try a morphological close using mri_morphology.

cheers

Bruce

‐‐‐ Original Message ‐‐‐
On August 2, 2018 3:15 PM, John Anderson  wrote:

> Dear Freesurfer experts,
> I would like to inquire if there is any command/method in FS6.0 that can help 
> to fill holes in a brain mask without dilating it?
>
> I would appreciate any advice!
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[Freesurfer] Filling holes

[John Anderson]

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Dear Freesurfer experts,
I would like to inquire if there is any command/method in FS6.0 that can help 
to fill holes in a brain mask without dilating it?

I would appreciate any advice!
John___
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[Freesurfer] Filling holes

[John Anderson]

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Dear Freesurfer experts,
I would like to inquire whether there is (are) any command(s) in FS6.0 that can 
help to fill holes in a brain mask without dilating it?

I would appreciate any advice,
John___
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Re: [Freesurfer] register mask to fsaverage

[John Anderson]

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Dear Dr Greve, I apologies if I was not clear.

I ran voxel-wise analysis between two groups. I thresholded the resultant 
statistical map at p<0.05 then I binarized it. This volumetric statistical map 
is in MNI152. I would like to move it to fsaverage then run group comparisons 
using it in the flag "--mask" in the command "mri_glmfit".  I highly appreciate 
if you guide me to the correct procedure.

John

If the roi.nii does not include your areas of interest, then they will be 
masked out. The mask you create with mri_vol2surf may not be very accurate 
since it uses volume-based operation.

On 7/26/18 5:19 PM, John Anderson wrote:

‐‐‐ Original Message ‐‐‐
On July 26, 2018 5:19 PM, John Anderson  wrote:

> Dear Dr Greve, thank you so much. kindly have one additional question and I 
> appreciate your response.
>
> I would like to move a mask from MNI152 to fsaverage so I can use it as a 
> mask in flag --mask in the command "mri_glmfit". Does this procedure reduces 
> the power of the analysis, meaning instead of correcting the the between 
> group analyses to the whole cortex. I would like to do it in the ROI? In my 
> analyses I see results when I correct for whole brain cortex. I mean when I 
> use the command:
> mri_glmfit --y data.nii.gz --fsgd fsgd.dat --C c.mtx --surf fsaverage lh 
> --cortex --glmdir dir
>
> I really lose these results when I use an ROI as a mask in the command 
> mri_glmfit as follows:
> mri_glmfit --y data.nii.gz --fsgd fsgd.dat --C c.mtx --surf fsaverage lh 
> --mask roi.nii --glmdir dir
> Thank you gain for any clarification,
> John
>
> Don't use --regheader, use --reg $FREESURFER_HOME/average/mni152.register.dat
>
> On 7/26/18 4:40 PM, John Anderson wrote:
>
> ‐‐‐ Original Message ‐‐‐
> On July 26, 2018 4:40 PM, John Anderson  wrote:
>
>> Dear Freesurfer experts,
>> I have mask in MNI152 space. I would like to register this mask to 
>> fsaverage. How can I do this registration. I am thinking of "mri_vol2surf" 
>> as follows:
>>
>> mri_vol2surf --mov mask.nii --mni152reg --regheader fsaverage --o 
>> mask_fsaverage.nii
>> Is this command correct?
>> Thank you for your valuable guidnace
>> John___
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Re: [Freesurfer] register mask to fsaverage

[John Anderson]

External Email - Use Caution

Dear Dr Greve, thank you so much. kindly have one additional question and I 
appreciate your response.

I would like to move a mask from MNI152 to fsaverage so I can use it as a mask 
in flag --mask in the command "mri_glmfit". Does this procedure reduces the 
power of the analysis, meaning instead of correcting the the between group 
analyses to the whole cortex. I would like to do it in the ROI? In my analyses 
I see results when I correct for whole brain cortex. I mean when I use the 
command:
mri_glmfit --y data.nii.gz --fsgd fsgd.dat --C c.mtx --surf fsaverage lh 
--cortex --glmdir dir

I really lose these results when I use an ROI as a mask in the command 
mri_glmfit as follows:
mri_glmfit --y data.nii.gz --fsgd fsgd.dat --C c.mtx --surf fsaverage lh --mask 
roi.nii --glmdir dir
Thank you gain for any clarification,
John

Don't use --regheader, use --reg $FREESURFER_HOME/average/mni152.register.dat

On 7/26/18 4:40 PM, John Anderson wrote:

‐‐‐ Original Message ‐‐‐
On July 26, 2018 4:40 PM, John Anderson  wrote:

> Dear Freesurfer experts,
> I have mask in MNI152 space. I would like to register this mask to fsaverage. 
> How can I do this registration. I am thinking of "mri_vol2surf" as follows:
>
> mri_vol2surf --mov mask.nii --mni152reg --regheader fsaverage --o 
> mask_fsaverage.nii
> Is this command correct?
> Thank you for your valuable guidnace
> John___
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[Freesurfer] register mask to fsaverage

[John Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I have mask in MNI152 space. I would like to register this mask to fsaverage. 
How can I do this registration. I am thinking of "mri_vol2surf" as follows:

mri_vol2surf --mov mask.nii --mni152reg --regheader fsaverage --o 
mask_fsaverage.nii
Is this command correct?
Thank you for your valuable guidnace
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Re: [Freesurfer] petsurfer

[John Anderson]

External Email - Use Caution

Dear Dr Greve, thank you for great responses and detailed explanation! Very 
highly appreciated!! Thank you for sharing that valuable manuscript!

Wish you all the best,
John

On 7/25/18 8:31 AM, John Anderson wrote:

Dear Petsurfer experts,

I used partsurfer in FS6 and had applied partial volume correction (PVC) on PET 
data. I followed the same steps as in wiki which was very well explained! Thank 
you!.

The analyses went fine... I would like to inquire about some issues, and I 
highly appreciate any clarification:

1. The flag --psf in "mri_gtmpvc": Is the value of "psf" means the amount of 
smoothing (fwhm in mm) that will be applied on the corrected maps? If I give 
"psf" a value of "zero", does this means that the corrected maps are no longer 
going to be smoothed? The motivation of the question is that I would like to 
smooth the images at the end of the analysis, so I can apply the amount of 
smoothing on the PVC images vs analysis involve non-pvc images.

It has nothing to do with applied smoothing but rather the amount of blurring 
incurred during the PET acquisition and reconstruction process. It models the 
blurring function as an isotropic Gaussian filter of the given FWHM. Any 
smoothing you apply will be applied later. Note that applying volume smoothing 
to PV-corrected data is invalid. Surface smoothing is the only valid way to 
smooth PVCed data.

2. For some of my group analyses, I don't see any difference between the 
groups. When I apply PVC using "mri_gtmpvc", I see difference in pathologically 
relevant regions, and vice versa for some other analyses where I see difference 
between the groups without PVC then the difference disappear following PVC. I 
highly appreciate if you please clarify why PVC can find results or eliminate 
findings. What is the idea of partial volume effect PVE in this case?

This is a big topic. See https://www.ncbi.nlm.nih.gov/pubmed/26915497. That 
paper shows that atrophy can make the apparent effect of age on FDG be bigger 
than it really is. This is because PVEs reduce the FDG signal in GM which tends 
to be the same direction as the actual effect (ie, the PVEs reinforce what is 
already there making it too big and too significant). For another tracer where 
one expects the uptake to go down with age or disease (eg, PiB), then PVEs can 
make effects go away.

3. Group analysis: following PVC, I used "mri_concat" to combine the images 
"?.mgx.gm.nii.gz", then I smoothed the final combined images using the flag 
"fwhm" in "mri_surf2surf". I used fwhm=3mm and then fwhm=6mm. For all analyses 
I can see clusters of difference between the groups at fwhm=3mm. For some 
analyses the difference disappears when I use fwhm=6mm . Is this till a partial 
volume effect even after applying  pvc or this is relevant to an extra 
smoothing effect which obscure the PET signal? is there any recommended fwhm 
value for PET images?

The FWHM you chose to smooth by for analysis purposes is somewhat arbitrary. 
The ideal FWHM depends on the size of the activation you are expecting, which 
you don't know until you do the analysis, which you can't do until you set the 
FWHM. If you have some idea about the size of the effect you expect, then you 
can set the FWHM to that level. Otherwise, people just fall back to typical 
values between 5-10.

Thank you for your guidance,

John

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‐‐‐ Original Message ‐‐‐
On July 25, 2018 8:31 AM, John Anderson  wrote:

> Dear Petsurfer experts,
> I used partsurfer in FS6 and had applied partial volume correction (PVC) on 
> PET data. I followed the same steps as in wiki which was very well explained! 
> Thank you!.
> The analyses went fine... I would like to inquire about some issues, and I 
> highly appreciate any clarification:
> 1. The flag --psf in "mri_gtmpvc": Is the value of "psf" means the amount of 
> smoothing (fwhm in mm) that will be applied on the corrected maps? If I give 
> "psf" a value of "zero", does this means that the corrected maps are no 
> longer going to be smoothed? The motivation of the question is that I would 
> like to smooth the images at the end of the analysis, so I can apply the 
> amount of smoothing on the PVC images vs analysis involve non-pvc images.
>
> 2. For some of my group analyses, I don't see any difference between the 
> groups. When I apply PVC using "mri_gtmpvc", I see difference in 
> pathologically relevant regions, and vice versa for some other analyses where 
> I see difference between the groups without PVC then the difference disappear 
> following PVC. I highly appreciate if you ple

[Freesurfer] petsurfer

[John Anderson]

External Email - Use Caution

Dear Petsurfer experts,
I used partsurfer in FS6 and had applied partial volume correction (PVC) on PET 
data. I followed the same steps as in wiki which was very well explained! Thank 
you!.
The analyses went fine... I would like to inquire about some issues, and I 
highly appreciate any clarification:
1. The flag --psf in "mri_gtmpvc": Is the value of "psf" means the amount of 
smoothing (fwhm in mm) that will be applied on the corrected maps? If I give 
"psf" a value of "zero", does this means that the corrected maps are no longer 
going to be smoothed? The motivation of the question is that I would like to 
smooth the images at the end of the analysis, so I can apply the amount of 
smoothing on the PVC images vs analysis involve non-pvc images.

2. For some of my group analyses, I don't see any difference between the 
groups. When I apply PVC using "mri_gtmpvc", I see difference in pathologically 
relevant regions, and vice versa for some other analyses where I see difference 
between the groups without PVC then the difference disappear following PVC. I 
highly appreciate if you please clarify why PVC can find results or eliminate 
findings. What is the idea of partial volume effect PVE in this case?

3. Group analysis: following PVC, I used "mri_concat" to combine the images 
"?.mgx.gm.nii.gz", then I smoothed the final combined images using the flag 
"fwhm" in "mri_surf2surf". I used fwhm=3mm and then fwhm=6mm. For all analyses 
I can see clusters of difference between the groups at fwhm=3mm. For some 
analyses the difference disappears when I use fwhm=6mm . Is this till a partial 
volume effect even after applying  pvc or this is relevant to an extra 
smoothing effect which obscure the PET signal? is there any recommended fwhm 
value for PET images?

Thank you for your guidance,
John___
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[Freesurfer] mri_binarize

[John Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I would like to inquire about the flag --subcort-gm in mri_binarize. It seems 
that the final product of this flag create a mask include the brain stem which 
is largely white matter. Why it was included in the subcortical gray matter 
structures?

Thanks for any clarification,
john___
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Re: [Freesurfer] Correct for sulcuses & ventricles size

[John Anderson]

External Email - Use Caution

Dear Dr Bruce,

Thank you for the response. Indeed, I was completely wrong, these represent a 
pathology and should not correct for!

Kindly, I have one additional question not relevant to the subject of this 
email. Is there any way in Freesurfer to create mask for the regions between 
the sulcuses. I want to compute PET signal in these regions and normalize for 
it.

Thank you so much!
John

Hi John

why do you want to correct for them? They likely represent a pathological 
process, so correcting for them may remove whatever effects you are looking 
for, no? The space between the sulci and the ventricle volume won't directly 
affect surface-based analysis, but of course the sulcal widening likely 
reflects cortical atrophy that will be

 cheers

Bruce

‐‐‐ Original Message ‐‐‐
On July 11, 2018 11:37 AM, John Anderson  wrote:

> Dear Freesurfer experts,
> I have two groups of subjects (healthy and patients). The patients have 
> different degrees of atrophy. Looking into the individual scans, the subjects 
> are largely different in the space between the sulcuses and the size of 
> ventricles. My questions are:
> 1. Is there any way to correct for these differences in the surface based 
> analysis?
> 2. Including eTIV covariate does it help in this case?
> 3. Does the resampling to "fsaverage" overcome the challenge of these 
> differences between the subjects?
>
> I appreciate any advice,
> John___
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[Freesurfer] Correct for sulcuses & ventricles size

[John Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I have two groups of subjects (healthy and patients). The patients have 
different degrees of atrophy. Looking into the individual scans, the subjects 
are largely different in the space between the sulcuses and the size of 
ventricles. My questions are:
1. Is there any way to correct for these differences in the surface based 
analysis?
2. Including eTIV covariate does it help in this case?
3. Does the resampling to "fsaverage" overcome the challenge of these 
differences between the subjects?

I appreciate any advice,
John___
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[Freesurfer] Visualization of surface based analysis results

[John Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I ran surface based analysis between two groups using PET surfer to study the 
difference in PET signal between two groups. I followed the same steps as in 
wiki and everything went fine. To visualize the final statistical maps, I used 
the command:
tksurfer fsaverage lh pial -overlay -overlay cache.th20.pos.sig.cluster.mgh

The report "cache.th20.pos.sig.cluster.summary" shows two significant 
structures (attached figure 1). Looking at the figure from the output of 
tksurfer (attached figure 2). I see significant results in the frontal lobe.

Please what I am doing wrong?
Your guidance is highly appreciated
John___
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Re: [Freesurfer] mri_Coreg or bbregister

[John Anderson]

External Email - Use Caution

Dear Dr Greve – I am immensely impressed with the results. thank you so much 
for all of your help!!!

Regards
john

You have to do it for each frame. Use reg.lta instead of reg.dat. You can apply 
it with mri_vol2vol --mov frame1.nii --reg reg1.lta --o frame1.reg.nii This 
will use trilinear interpolation by default, but that is probably ok here.

‐‐‐ Original Message ‐‐‐
On July 3, 2018 2:29 PM, John Anderson  wrote:

> Hi Dr Greve,
> If the individual PET frames are named: frame1.nii frame2.nii, frame3.nii ... 
>  frame10.nii, and the mean for all the ten frames is "frames_mean.nii"
>
> I ran mri_corg on one of the fames as follows:
> mri_coreg --mov frame1.nii --ref frames_mean.nii --reg reg.dat.
>
> Do I need to run the same command on every frame, or just apply reg.dat on 
> all the frames. If applying reg.dat on all the frames is the correct 
> procedure. How can I do it?
>
> Your guidance is highly appreciated.
> John
>
> mri_coreg is the right one for that job
>
> ‐‐‐‐‐‐‐ Original Message ‐‐‐
> On July 3, 2018 1:51 PM, John Anderson  wrote:
>
>> Dear Freesurfer experts,
>> I have ten PET frames for every subject in my database. these frames 
>> represent specific time during PET acquisition. Due to head motion during 
>> acquisition the frames are not fully overlapped on top of each other. I 
>> created template represent the mean of the ten frames. I would like to 
>> register each low res frame to this low res template. Which tool in 
>> Freesurfer is more robust to achieve this goal.
>> Any additional suggestions are highly appreciated
>> Thanks
>> John___
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Re: [Freesurfer] mri_Coreg or bbregister

[John Anderson]

External Email - Use Caution

Hi Dr Greve,
If the individual PET frames are named: frame1.nii frame2.nii, frame3.nii ... 
 frame10.nii, and the mean for all the ten frames is "frames_mean.nii"

I ran mri_corg on one of the fames as follows:
mri_coreg --mov frame1.nii --ref frames_mean.nii --reg reg.dat.

Do I need to run the same command on every frame, or just apply reg.dat on all 
the frames. If applying reg.dat on all the frames is the correct procedure. How 
can I do it?

Your guidance is highly appreciated.
John

mri_coreg is the right one for that job

‐‐‐ Original Message ‐‐‐
On July 3, 2018 1:51 PM, John Anderson  wrote:

> Dear Freesurfer experts,
> I have ten PET frames for every subject in my database. these frames 
> represent specific time during PET acquisition. Due to head motion during 
> acquisition the frames are not fully overlapped on top of each other. I 
> created template represent the mean of the ten frames. I would like to 
> register each low res frame to this low res template. Which tool in 
> Freesurfer is more robust to achieve this goal.
> Any additional suggestions are highly appreciated
> Thanks
> John___
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[Freesurfer] mri_Coreg or bbregister

[John Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I have ten PET frames for every subject in my database. these frames represent 
specific time during PET acquisition. Due to head motion during acquisition the 
frames are not fully overlapped on top of each other. I created template 
represent the mean of the ten frames. I would like to register each low res 
frame to this low res template. Which tool in Freesurfer is more robust to 
achieve this goal.
Any additional suggestions are highly appreciated
Thanks
John___
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Re: [Freesurfer] manual edits

[John Anderson]

External Email - Use Caution

Hi Dr Bruce,
I ran surface based analysis between one subject and a group of controls. The 
problem is that I don't expect any difference in this region at least visually 
(i.e. by looking at the CC in controls and compare it with the subject's data). 
I will upload the mages for your consideration and thank you for the help.

John 


​Sent with ProtonMail Secure Email.​

‐‐‐ Original Message ‐‐‐

On May 30, 2018 11:42 AM, Bruce Fischl  wrote:

> Hi John
> 
> is this causing a problem for you? What type of analysis do you want to
> 
> do that is impacted by this? If you upload the subject we will take a look,
> 
> but these regions are typically excluded from the surface analysis as they
> 
> are non-cortical anyway.
> 
> cheers
> 
> Bruce
> 
> On Wed, 30 May 2018, John Anderson wrote:
> 
> >External Email - Use Caution 
> > 
> > 
> > Hi Dr Bruce.
> > 
> > I highly appreciate your quick response. kindly see attached is another 
> > view. The boundaries of the corpus callosum are not correctly defined on 
> > multiple slices. Can this be fixed by setting control points in the CC 
> > regions?
> > 
> > Thanks
> > 
> > ​Sent with ProtonMail Secure Email.​
> > 
> > ‐‐‐ Original Message ‐‐‐
> > 
> > On May 30, 2018 11:27 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
> > 
> > > Hi John
> > > 
> > > I'm not sure I understand exactly what you are referring to. We
> > > 
> > > automatically fill in the ventricles so that they are contained within
> > > 
> > > the interior of the ?h.white surfaces. Is that what you thought was
> > > 
> > > incorrect?
> > > 
> > > cheers
> > > 
> > > Bruce
> > > 
> > > On Wed, 30 May 2018, John Anderson wrote:
> > > 
> > > > External Email - Use Caution
> > > > 
> > > > Dear FS experts,
> > > > 
> > > > My question is very basic and I appreciate your help.
> > > > 
> > > > I ran recon-all on a low quality T1 image. I'd like to fix the 
> > > > segmentation error (attached).
> > > > 
> > > > Wm.mgz seems to be fine and the wm intensity is ~110. Can this error be 
> > > > fixed by setting control points in the region then re
> > > > 
> > > > run the command :
> > > > 
> > > > recon-all -s  -autorecon2-cp -autorecon3
> > > > 
> > > > Thanks for any advice
> > > > 
> > > > John
> > > 
> > > 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] manual edits

[John Anderson]

External Email - Use Caution

Hi Dr Bruce.
I highly appreciate your quick response. kindly see attached is another view. 
The boundaries of the corpus callosum are not correctly defined on multiple 
slices. Can this be fixed by setting control points in the CC regions?

Thanks



​Sent with ProtonMail Secure Email.​

‐‐‐ Original Message ‐‐‐

On May 30, 2018 11:27 AM, Bruce Fischl  wrote:

> Hi John
> 
> I'm not sure I understand exactly what you are referring to. We
> 
> automatically fill in the ventricles so that they are contained within
> 
> the interior of the ?h.white surfaces. Is that what you thought was
> 
> incorrect?
> 
> cheers
> 
> Bruce
> 
> On Wed, 30 May 2018, John Anderson wrote:
> 
> > External Email - Use Caution
> > 
> > Dear FS experts,
> > 
> > My question is very basic and I appreciate your help.
> > 
> > I ran recon-all on a low quality T1 image. I'd like to fix the segmentation 
> > error (attached).
> > 
> > Wm.mgz seems to be fine and the wm intensity is ~110. Can this error be 
> > fixed by setting control points in the region then re
> > 
> > run the command :
> > 
> > recon-all -s  -autorecon2-cp -autorecon3
> > 
> > Thanks for any advice
> > 
> > John
> 
> 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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[Freesurfer] manual edits

[John Anderson]

External Email - Use Caution

Dear FS experts,
My question is very basic and I appreciate your help.
I ran recon-all on a low quality T1 image. I'd like to fix the segmentation 
error (attached).

Wm.mgz seems to be fine and the wm intensity is ~110. Can this error be fixed 
by setting control points in the region then re run the command :
recon-all -s  -autorecon2-cp -autorecon3

Thanks for any advice
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Re: [Freesurfer] PET partial volume correction

[John Anderson]

Dear Dr Greve,
Thank you so much for the quick response.

Just to confirm that I understood the procedure correctly. The analysis is 
volume based (i.e. voxel-wise) for the subcortical structures using mask 
created by freesurfer's "mri_binarize" for these regions.

Correct?

 Original Message 
On January 18, 2018 4:34 PM, John Anderson <john.ande...@protonmail.com> wrote:
It is volume-based for subcortical

On 1/12/18 8:17 AM, John Anderson wrote:

> Dear Dr Greeve,
> I interestingly read the manuscript "Different partial volume correction 
> methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank 
> you for publishing this data.
>
> I understood from this paper that he recommended stream for PVC is to correct 
> the PET images using Muller-Gartner method then feed the corrected maps into 
> three group level analyses: surface based for left and right hemispheres then 
> for subcortical regions..
>
> My question is about the subcortical analysis: To describe this analysis, is 
> it a volumetric analysis for subcortical gray matter, or surface based?
>
> I am sorry if my questions is basics, I don't have good experience in 
> freesurfer so I want to be sure that I am using the correct terms.
>
> Thanks you for any advice!
> John___
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[Freesurfer] mri_coreg

[John Anderson]

Dear FS developers,
Are there any versions of "mri_coreg" that allows to output the registered 
images. I mean flag "--out or -o" similar to spmregister?

Thanks for any guidance
John___
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[Freesurfer] PET partial volume correction

[John Anderson]

Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction 
methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank 
you for publishing this data.

I understood from this paper that he recommended stream for PVC is to correct 
the PET images using Muller-Gartner method then feed the corrected maps into 
three group level analyses: surface based for left and right hemispheres then 
for subcortical regions..

My question is about the subcortical analysis: To describe this analysis, is it 
a volumetric analysis for subcortical gray matter, or surface based?

I am sorry if my questions is basics, I don't have good experience in 
freesurfer so I want to be sure that I am using the correct terms.

Thanks you for any advice!
John___
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[Freesurfer] PET partial volume correction

[John Anderson]

Dear Dr Greeve,
I interestingly read the manuscript "Different partial volume correction 
methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank 
you for publishing this data.

I understood from this paper that he recommended stream for PVC is to correct 
the PET images using Muller-Gartner method then feed the corrected maps into 
three group level analyses: surface based for left and right hemispheres then 
for subcortical regions..

My question is about the subcortical analysis: To describe this analysis, is it 
a volumetric analysis for subcortical gray matter, or surface based?

I am sorry if my questions is basics, I don't have good experience in 
freesurfer so I want to be sure that I am using the correct terms.

Thanks you for any advice!
J___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] combining masks

[John Anderson]

Yes!! this worked. Thank you so much!

I was afraid of that. You will need to either map wmparc to the brainstem space 
or the brainstem into the wmparc. Probably better to do the first. You can use 
mri_label2vol with --seg wmparc.mgz --temp brainstem.mgz --regheader wmparc.mgz 
--o wmparc.in-brainstem.mgz
swif�,7�&

>  Original Message 
> Subject: Re: combining masks
> Local Time: January 10, 2018 11:54 AM
> UTC Time: January 10, 2018 4:54 PM
> From: john.ande...@protonmail.com
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>
> Dear Dr Greeve,
> Thank you very much for the quick and detailed response.
> Before your response, I tried fslmaths instead of fslcalc and I got error 
> message complains about misorientation between the input masks.
>
> Now, I tried fslcalc and it failed as well to combine the masks due to a 
> mismatch sizes!
> Any suggestions are highly appreciated?
>
> you'll need to do it in 3 steps
>
> mri_binarize --i wmparc.mgz --match 1024 2024 3024 4024  --o wmparc.mask.mgz
>
> mri_binarize --i brainstemSsLabels.v10.mgz --match 173 --o bs.mask.mgz
>
> fscalc wmparc.mask.mgz and bs.mask.mgz -o final.mask.mgz
>
> The only problem will be if the brainstem seg is higher res than wmpar
>
> On 01/10/2018 11:10 AM, John Anderson wrote:
>
>> Dear Freesurfer experts,
>
>> I want to create mask for the midbrain and the precentral gyrus.
>
>> I used FSV6 to do the reconstruction. Then I used the flag
>
>> -brainstem-structures in recon-all to segment the brain stem.
>
>> How can I create _one mask_ that include structures from wmpac.mgz and
>
>> brainstemSsLabels.v10.mgz for instance I want to use mri_binarize to
>
>> create one mask contains the following labels
>
>> 1024 2024 3024 4024 from wmpar.mgz and 173 from
>
>> brainstemSsLabels.v10.mgz
>
>>
>
>> Any advice you provide is highly appreciated.
>
>> Thanks
>
>> John
>
>>  Original Message 
>> Subject: combining masks
>> Local Time: January 10, 2018 11:10 AM
>> UTC Time: January 10, 2018 4:10 PM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>
>> Dear Freesurfer experts,
>> I want to create mask for the midbrain and the precentral gyrus.
>> I used FSV6 to do the reconstruction. Then I used the flag 
>> -brainstem-structures in recon-all to segment the brain stem.
>> How can I create one mask that include structures from wmpac.mgz and 
>> brainstemSsLabels.v10.mgz for instance
>> I want to use mri_binarize to create one mask contains the following labels
>> 1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz
>>
>> Any advice you provide is highly appreciated.
>> Thanks
>> John___
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Re: [Freesurfer] combining masks

[John Anderson]

Dear Dr Greeve,
Thank you very much for the quick and detailed response.
Before your response, I tried fslmaths instead of fslcalc and I got error 
message complains about misorientation between the input masks.

Now, I tried fslcalc and it failed as well to combine the masks due to a 
mismatch sizes!
Any suggestions are highly appreciated?

you'll need to do it in 3 steps

mri_binarize --i wmparc.mgz --match 1024 2024 3024 4024  --o wmparc.mask.mgz

mri_binarize --i brainstemSsLabels.v10.mgz --match 173 --o bs.mask.mgz

fscalc wmparc.mask.mgz and bs.mask.mgz -o final.mask.mgz

The only problem will be if the brainstem seg is higher res than wmpar

On 01/10/2018 11:10 AM, John Anderson wrote:

> Dear Freesurfer experts,

> I want to create mask for the midbrain and the precentral gyrus.

> I used FSV6 to do the reconstruction. Then I used the flag

> -brainstem-structures in recon-all to segment the brain stem.

> How can I create _one mask_ that include structures from wmpac.mgz and

> brainstemSsLabels.v10.mgz for instance I want to use mri_binarize to

> create one mask contains the following labels

> 1024 2024 3024 4024 from wmpar.mgz and 173 from

> brainstemSsLabels.v10.mgz

>

> Any advice you provide is highly appreciated.

> Thanks

> John

>  Original Message 
> Subject: combining masks
> Local Time: January 10, 2018 11:10 AM
> UTC Time: January 10, 2018 4:10 PM
> From: john.ande...@protonmail.com
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>
> Dear Freesurfer experts,
> I want to create mask for the midbrain and the precentral gyrus.
> I used FSV6 to do the reconstruction. Then I used the flag 
> -brainstem-structures in recon-all to segment the brain stem.
> How can I create one mask that include structures from wmpac.mgz and 
> brainstemSsLabels.v10.mgz for instance
> I want to use mri_binarize to create one mask contains the following labels
> 1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz
>
> Any advice you provide is highly appreciated.
> Thanks
> John___
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[Freesurfer] combining masks

[John Anderson]

Dear Freesurfer experts,
I want to create mask for the midbrain and the precentral gyrus.
I used FSV6 to do the reconstruction. Then I used the flag 
-brainstem-structures in recon-all to segment the brain stem.
How can I create one mask that include structures from wmpac.mgz and 
brainstemSsLabels.v10.mgz for instance
I want to use mri_binarize to create one mask contains the following labels
1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz

Any advice you provide is highly appreciated.
Thanks
John___
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[Freesurfer] extra brain tiussue

[John Anderson]

Dear FS experts,
I want to extra the extra brain tissue. Is it correct to subtract orig.mgz from 
aparc+aseg?
Is this provide accurate estimates forrhe space between the brain tissue and 
the skull.
Kindly, do you suggest me better solution?
Thanks for any advice!
J___
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[Freesurfer] mri_nlfilter

[John Anderson]

Dear Dr Bruce,
Kindly, I have question regarding the command "mri_nlfilter". I am sorry if my 
questions is simple, but I highly appreciate any explanation to improve my 
understanding.

I see in the man list of the command "mri_nlfilter" that it can apply Gaussian 
filtering and blurring kernell.
What is the difference between Gaussian smoothing and blurring. For example in 
PET images we used to smooth the images to improve SNR. Does blurring apply 
something similar and can be helpful to improve SNR.

Thanks for any clarification!
J___
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Re: [Freesurfer] cortical thickness smoothing

[John Anderson]

Dear Dr Greve thank you so much for the advice.

Kindly, I have one addition question and I highly appreciate your feedback!
Smoothing on surface is very interesting and it is really more accurate than 
applying the Gaussian smoothing directly on volumetric images. I don't see any 
aggressive shifts in the signal when I smooth on surface! In this context, I 
want to know if the following procedure is legitimate:

To  smooth PET volumetric images. I am thinking of using "mri_vol2surf" to 
sample and smooth the PET images on surface. Can I then use "mri_surf2vol" to 
move the smoothed images on surface to volume. How about the subcortical 
regions- is the smoothing on surface applicable for the whole brain, or just 
for the regions between pial/white?

You have to sample the volumetric PET data onto the surface

(mri_vol2surf) and then smooth it there (mri_surf2surf or mris_fwhm).

On 12/12/2017 11:23 AM, John Anderson wrote:

> Dear Dr Bruce, I highly appreciate the response.

> I want to smooth PET volumetric images, when I use "fslmaths", it

> shifts the signal from the cortex to the underlying structures. I

> think (depending on wiki) that Freesurfer handles this issue by

> smoothing on sphere. Which is the recommendded stream in PETsurfer.

>

> I am wondering if there are any commands within Freesurfer that can be

> used to smooth volumtric PET images without taking the average signal

> of the neighboring voxels (like in Gaussian smoothing).

>

> Also, I have question about mri_fwhm:

> what is the difference between the flags (--smooth-only; --fwhm). I am

> aware that "mri_fwhm" is very well explained in FS wiki, but I was

> unable to exactly understand the difference. For instance when I use

> the flag --smooth-only the output image is somehow similar to the

> input image. Is Gaussian in this cases ~1

mri_fwhm (and mris_fwhm) where initially developed to measure the FWHM

but I extended it to be able to apply smoothing (--fwhm) as well as

measure the smoothness. The --smooth-only says to not do the FWHM

estimate (just smooth it).

>

> Thanks in advance!

> J

>

>

>

>

>

>

>>  Original Message 

>> Subject: Re: [Freesurfer] cortical thickness smoothing

>> Local Time: December 12, 2017 10:38 AM

>> UTC Time: December 12, 2017 3:38 PM

>> From: fis...@nmr.mgh.harvard.edu

>> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support

>> list <freesurfer@nmr.mgh.harvard.edu>

>>

>> Hi John

>>

>> I don't think fslmaths takes a surface topology so they won't be the same

>> (mri_surf2surf smooths within the surface and fslmaths smooths in the

>> volume I believe)

>>

>> cheers

>> Bruce

>>

>>

>> On Tue, 12 Dec 2017, John Anderson wrote:

>>

>> Dear Freesurfer experts,

>> I ran recon-all with the flag -qcache to generate smoothed

>> cortical thickness maps.

>> In order to check how the flag "-qcache" is smoothing the

>> cortical thickness data. I looked into the

>> file $subj_dir/scripts/recon-all.log" which showed that the

>> following command was applied:

>> mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval

>> lh.sulc.fsaverage.mgh --tval

>> lh.sulc.fwhm5.fsaverage.mgh --cortex

>> Please I want to know whether the flag "--fwhm" applies similar

>> smoothing method to the smoothing

>> output of the command "fslmaths":

>> fslmaths  -kernel gauss 2.213 -fmean

>>  -odt float

>> I want to smooth two different modality-images using the cortical

>> thickness smoothing method.

>> Thank you for any advice!

>> John

>>

>>

>>

>> 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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--

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Phone Number: 617-724-2358

Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.m

Re: [Freesurfer] cortical thickness smoothing

[John Anderson]

Dear Dr Bruce, I highly appreciate the response.
I want to smooth PET volumetric images, when I use "fslmaths", it shifts the 
signal from the cortex to the underlying structures. I think (depending on 
wiki) that Freesurfer handles this issue by smoothing on sphere. Which is the 
recommendded stream in PETsurfer.

I am wondering if there are any commands within Freesurfer that can be used to 
smooth volumtric PET images without taking the average signal of the 
neighboring voxels (like in Gaussian smoothing).

Also, I have question about mri_fwhm:
what is the difference between the flags (--smooth-only; --fwhm). I am aware 
that "mri_fwhm" is very well explained in FS wiki, but I was unable to exactly 
understand the difference. For instance when I use the flag --smooth-only the 
output image is somehow similar to the input image. Is Gaussian in this cases ~1

Thanks in advance!
J

>  Original Message 
> Subject: Re: [Freesurfer] cortical thickness smoothing
> Local Time: December 12, 2017 10:38 AM
> UTC Time: December 12, 2017 3:38 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list 
> <freesurfer@nmr.mgh.harvard.edu>
>
> Hi John
>
> I don't think fslmaths takes a surface topology so they won't be the same
> (mri_surf2surf smooths within the surface and fslmaths smooths in the
> volume I believe)
>
> cheers
> Bruce
>
> On Tue, 12 Dec 2017, John Anderson wrote:
>
>> Dear Freesurfer experts,
>> I ran recon-all with the flag -qcache to generate smoothed cortical 
>> thickness maps.
>> In order to check how the flag "-qcache" is smoothing the cortical thickness 
>> data. I looked into the
>> file $subj_dir/scripts/recon-all.log" which showed that the following 
>> command was applied:
>> mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval 
>> lh.sulc.fsaverage.mgh --tval
>> lh.sulc.fwhm5.fsaverage.mgh --cortex
>> Please I want to know whether the flag "--fwhm" applies similar smoothing 
>> method to the smoothing
>> output of the command "fslmaths":
>> fslmaths  -kernel gauss 2.213 -fmean  
>> -odt float
>> I want to smooth two different modality-images using the cortical thickness 
>> smoothing method.
>> Thank you for any advice!
>> John
>
> 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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[Freesurfer] cortical thickness smoothing

[John Anderson]

Dear Freesurfer experts,
I ran recon-all with the flag -qcache to generate smoothed cortical thickness 
maps.
In order to check how the flag "-qcache" is smoothing the cortical thickness 
data. I looked into the file $subj_dir/scripts/recon-all.log" which showed that 
the following command was applied:

mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval 
lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex

Please I want to know whether the flag "--fwhm" applies similar smoothing 
method to the smoothing output of the command "fslmaths":

fslmaths  -kernel gauss 2.213 -fmean  -odt 
float

I want to smooth two different modality-images using the cortical thickness 
smoothing method.

Thank you for any advice!
John___
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[Freesurfer] power analysis

[John Anderson]

Dear Freesurfer exerts,
I read sentences similar to this one in multiple publications (e.g. 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500581/)
"Power analyses were carried out using vertex-wise variance estimates from the 
coregistered cortical thickness maps, systematically varying processing 
parameters. "

Please how can I use freesurfer to do power analysis. Cortical thickness 
(vertex-based analysis) is very well documented in Freesurfer wiki. How can I 
use the output of this analysis (i.e. gamma.mgh and the gammavar.mgh ) to 
measure the power.

I highly appreciate any advice.
John___
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[Freesurfer] subtract CSF

[John Anderson]

Dear FS experts,
I want to create mask from the atlas "aparc.DKTatlas+aseg.mgz". I need the mask 
to be free of any CSF or ventricles components. Is there any way to subtract 
these labels (CSF and ventricles) from the atlas "aparc.DKTatlas+aseg.mgz".

Thank you for your help
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[Freesurfer] mri_binarize

[John Anderson]

Dear FS experts,
I want to use mri_binarize to create (binarized and free of CSF and ventricles) 
mask from "aparc.DKTatlas+aseg". How can I substract CSF and ventricles from 
teh atlas using mri_binarize?

Thanks
John___
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[Freesurfer] transformation matrix

[John Anderson]

Dear FS experts,
Is there any transformation matrix between the files /mri/orig.mgz and the file 
/mri/rawavg.mgz

Please advice!
John___
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Re: [Freesurfer] FA to MNI

[John Anderson]

Dear Dr Bruce,
Thank you so much for the quick response. Yes I used bbregister, but I don't 
know how to transform correctly.
I appreciate your guidance!

peace
J

>  Original Message 
> Subject: Re: [Freesurfer] FA to MNI
> Local Time: November 30, 2017 3:54 PM
> UTC Time: November 30, 2017 8:54 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list 
> <freesurfer@nmr.mgh.harvard.edu>
>
> Hi John
>
> if your FA map is registered to the structurals (e.g. using bbregister)
> then you would just compose that transform with the talairach.xfm in the
> subject's mri/transforms dir.
>
> cheers
> Bruce
> On Thu, 30 Nov 2017, John Anderson wrote:
>
>> Dear Freesurfer experts,
>> I want to register FA map in subject space to MNI. How can I do it using 
>> freesurfer tools?
>> Any advice is highly appreciated!
>> J
>
> 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 
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> but does not contain patient information, please contact the sender and 
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[Freesurfer] FA to MNI

[John Anderson]

Dear Freesurfer experts,
I want to register FA map in subject space to MNI. How can I do it using 
freesurfer tools?

Any advice is highly appreciated!
J___
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[Freesurfer] mean cortical thickness map

[John Anderson]

Dear Freesurfer community,
I want to visualize the mean cortical thickness map of 20 subjects. I ran the 
command recon-all on the the T1 images. How can I visualize the mean cortical 
thickness of one group.

Thanks for any advice
John___
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[Freesurfer] surface based correlation analysis

[John Anderson]

Dear Dr Doug,
I want to study the relationship between PET signal measured as the mean signal 
of the whole cortex and gray matter volume to find regions of association 
between gray matter atrophy and PET signal.

In this case I will need to run surface based analysis and the FSGD file must 
be "One Group, One Covariate" is this correct?

Thanks for any suggestions/ advice!
John___
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[Freesurfer] 3D visualization

[John Anderson]

Dear FS experts,
Are there any tools in freesurfer for 3D visualization (e.g. glass brain)? Any 
recommendations are appreciated
Thanks
John___
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Re: [Freesurfer] BA Labels

[John Anderson]

It seems that this command doesn't accept input files. Are there any commands 
in Freesurfer that can do similar job?

>  Original Message 
> Subject: Re: [Freesurfer] BA Labels
> Local Time: September 13, 2017 3:11 PM
> UTC Time: September 13, 2017 7:11 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>
> Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>
> you should be able to use mris_anatomical_stats I believe
>
> cheers
> Bruce
> On Wed, 13 Sep
> 2017, John Anderson wrote:
>
>> Thank you Dr Bruce,
>> The stat values for every BA are generated using the command 
>> mris_anatomical_stats. I found this
>> command in the stats file for one of the BAs.
>> In this stats file I see values for gray  matter volume, thickness ,... etc.
>>
>> If I move SUV map or FA map to surface using the command mri_vol2surf. Then 
>> how can I generate the
>> SUV and FA values from the BA labels similar to what the command 
>> mris_anatomical_stats does?
>>
>>
>>  Original Message 
>> Subject: Re: [Freesurfer] BA Labels
>> Local Time: September 13, 2017 2:57 PM
>> UTC Time: September 13, 2017 6:57 PM
>> From: fis...@nmr.mgh.harvard.edu
>> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list
>> <freesurfer@nmr.mgh.harvard.edu>
>>
>> Hi John
>>
>> if you have run recon-all you should have a bunch of ex vivo BA labels in
>> the label dir.
>>
>> cheers
>> Bruce
>> On Wed, 13 Sep 2017, John Anderson wrote:
>>
>> > Dear FS experts,
>> > I have SUV maps for subjects within two groups. I moved these SUV maps 
>> > into surface then I
>> > concatenated the images in the order of two groups then I used the 
>> > compiled file in a glm
>> analysis
>> > to check the difference between the two groups.
>> >
>> > I aim to use V1 Atlas to derive the SUV values from the BA labels. I am 
>> > not sure how to
>> utilize
>> > these labels in such analysis. In this context I have two questions:
>> >
>> > 1. Can these label be converted to ROIs similar to the ROIs derived from 
>> > wmpar.mgz using the
>> command
>> > mri_binarize?
>> >
>> > 2. in WIKI it was mentioned that the command "recon-all -s subjid 
>> > -label_v1" output the stat
>> values
>> > for every BA label. How can I derive similar stats from the SUV maps in 
>> > the compiled file.
>> >
>> >
>> > Thanks in advance
>> > John
>> >
>> >
>>
>>
>> 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] BA Labels

[John Anderson]

Thank you Dr Bruce,
The stat values for every BA are generated using the command 
mris_anatomical_stats. I found this command in the stats file for one of the 
BAs.
In this stats file I see values for gray  matter volume, thickness ,... etc.

If I move SUV map or FA map to surface using the command mri_vol2surf. Then how 
can I generate the SUV and FA values from the BA labels similar to what the 
command mris_anatomical_stats does?

>  Original Message 
> Subject: Re: [Freesurfer] BA Labels
> Local Time: September 13, 2017 2:57 PM
> UTC Time: September 13, 2017 6:57 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list 
> <freesurfer@nmr.mgh.harvard.edu>
>
> Hi John
>
> if you have run recon-all you should have a bunch of ex vivo BA labels in
> the label dir.
>
> cheers
> Bruce
> On Wed, 13 Sep 2017, John Anderson wrote:
>
>> Dear FS experts,
>> I have SUV maps for subjects within two groups. I moved these SUV maps into 
>> surface then I
>> concatenated the images in the order of two groups then I used the compiled 
>> file in a glm analysis
>> to check the difference between the two groups.
>>
>> I aim to use V1 Atlas to derive the SUV values from the BA labels. I am not 
>> sure how to utilize
>> these labels in such analysis. In this context I have two questions:
>>
>> 1. Can these label be converted to ROIs similar to the ROIs derived from 
>> wmpar.mgz using the command
>> mri_binarize?
>>
>> 2. in WIKI it was mentioned that the command "recon-all -s subjid -label_v1" 
>> output the stat values
>> for every BA label. How can I derive similar stats from the SUV maps in the 
>> compiled file.
>>
>>
>> Thanks in advance
>> John
>>
>>
>
> 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
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[Freesurfer] BA Labels

[John Anderson]

Dear FS experts,
I have SUV maps for subjects within two groups. I moved these SUV maps into 
surface then I concatenated the images in the order of two groups then I used 
the compiled file in a glm analysis to check the difference between the two 
groups.

I aim to use V1 Atlas to derive the SUV values from the BA labels. I am not 
sure how to utilize these labels in such analysis. In this context I have two 
questions:

1. Can these label be converted to ROIs similar to the ROIs derived from 
wmpar.mgz using the command mri_binarize?

2. in WIKI it was mentioned that the command "recon-all -s subjid -label_v1" 
output the stat values for every BA label. How can I derive similar stats from 
the SUV maps in the compiled file.

Thanks in advance
John___
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[Freesurfer] QC cortical thickness measurements

[John Anderson]

Dear FS experts,
my apologizes if my question is a simple one. I am new to Freesurfer and I 
appreciate if you help me.
After running recon-all on a T1 image I reached the final step and the analysis 
ran smoothly without any issues.. Now what I need to check in the output images 
to be sure that the cortical thickness measurements are correct and ready for 
cortical thickness group analysis like the one explained int this page 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?

If you can share any guide or a workflow sheet that can be followed to check 
the recons and the cortical thickness measurements systematically it will be 
highly appreciated!

Thanks in advance for any help!!
John___
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Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

[John Anderson]

Thank you Dr Bruce,
It seems that FS5.3 doesn't output this file. I just checked many recons 
processed using FS5.3 without FLAIR and the file "aparc.DKTatlas+aseg.mgz" is 
missing in all these recons.
I see aseg.mgz, aseg+aparc.mgz and wmparc.mgz

>  Original Message 
> Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
> Local Time: August 31, 2017 4:04 PM
> UTC Time: August 31, 2017 8:04 PM
> From: fis...@nmr.mgh.harvard.edu
> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list 
> <freesurfer@nmr.mgh.harvard.edu>
> "Boyd, Emma" <ebo...@mgh.harvard.edu>
>
> Hi John
>
> the atlas isn"t flair-based (and is done before the flair processing). I
> thought we always generated both (plus Christophe"s for 3 total), so I"m
> a bit confused
> cheers
> Bruce
> On Thu, 31 Aug 2017, John Anderson wrote:
>
>> Hi Emma,
>> Thank you for your response.
>> I am running my recons using V5.3 and V6.0
>> In the data base I have ~200  T1 images and for some I have FLAIR images.
>> When I run recon all with the flag FLAIR I get the file 
>> "aparc.DKTatlas+aseg.mgz" in FS5.3 and FS6.0
>> If I run recon-all without the flag FLAIR i don"t see the file 
>> aparc.DKTatlas+aseg.mgz
>> as an output of FS5.3 or FS6.0
>>
>> I am a bit confused about this!! Is this atlas FALIR-based or I am doing 
>> something wrong?!
>>
>>
>>
>>
>>  Original Message 
>> Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
>> Local Time: August 31, 2017 3:11 PM
>> UTC Time: August 31, 2017 7:11 PM
>> From: ebo...@mgh.harvard.edu
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, John Anderson
>> <john.ande...@protonmail.com>
>>
>>
>> Hi John,
>>
>> Which version of FreeSurfer are you running?
>>
>>
>> Emma
>>
>>
>> -
>>
>> Emma Boyd
>>
>> Research Technician II
>>
>> Laboratory for Computational Neuroimaging
>>
>> Martinos Center for Biomedical Imaging
>>
>> 
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> <freesurfer-boun...@nmr.mgh.harvard.edu> on
>> behalf of John Anderson <john.ande...@protonmail.com>
>> Sent: Thursday, August 31, 2017 12:17 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
>>
>> Dear experts,
>> looking into the output of Freesurfer in this
>> page https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
>> I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Is this 
>> atlas can be
>> generated with the presence of FLAIR images.
>>
>> When i run recon-all without FLAIR or T2 I don"t see this atlas!! Is this 
>> atlas FLAIR -based?
>>
>> thank you for any clarification
>> John
>>
>>  Original Message 
>> Subject: aparc.DKTatlas+aseg.mgz
>> Local Time: August 30, 2017 7:49 PM
>> UTC Time: August 30, 2017 11:49 PM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>
>> Dear experts,
>> looking into the output of Freesurfer in this
>> page https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
>> I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Do I need 
>> FLAIR
>> images to get this file.
>>
>> I ran the command recon-all --s subj --all and I can";t find this file
>>
>>
>> thank you for any clarification
>> John
>>
>>
>>
>> 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] aparc.DKTatlas+aseg.mgz

[John Anderson]

Hi Emma,
Thank you for your response.
I am running my recons using V5.3 and V6.0
In the data base I have ~200  T1 images and for some I have FLAIR images.
When I run recon all with the flag FLAIR I get the file 
"aparc.DKTatlas+aseg.mgz" in FS5.3 and FS6.0
If I run recon-all without the flag FLAIR i don't see the file 
aparc.DKTatlas+aseg.mgz
as an output of FS5.3 or FS6.0

I am a bit confused about this!! Is this atlas FALIR-based or I am doing 
something wrong?!

>  Original Message 
> Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
> Local Time: August 31, 2017 3:11 PM
> UTC Time: August 31, 2017 7:11 PM
> From: ebo...@mgh.harvard.edu
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, John Anderson 
> <john.ande...@protonmail.com>
>
> Hi John,
>
> Which version of FreeSurfer are you running?
>
> Emma
>
> -
>
> Emma Boyd
>
> Research Technician II
>
> Laboratory for Computational Neuroimaging
>
> Martinos Center for Biomedical Imaging
>
> ---
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of John Anderson 
> <john.ande...@protonmail.com>
> Sent: Thursday, August 31, 2017 12:17 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] aparc.DKTatlas+aseg.mgz
>
> Dear experts,
> looking into the output of Freesurfer in this page 
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
> I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Is this 
> atlas can be generated with the presence of FLAIR images.
>
> When i run recon-all without FLAIR or T2 I don't see this atlas!! Is this 
> atlas FLAIR -based?
>
> thank you for any clarification
> John
>
>>  Original Message 
>> Subject: aparc.DKTatlas+aseg.mgz
>> Local Time: August 30, 2017 7:49 PM
>> UTC Time: August 30, 2017 11:49 PM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>
>> Dear experts,
>> looking into the output of Freesurfer in this page 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
>> I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Do I need 
>> FLAIR images to get this file.
>>
>> I ran the command recon-all --s subj --all and I can';t find this file
>>
>> thank you for any clarification
>> John
>
> 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
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Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

[John Anderson]

Dear experts,
looking into the output of Freesurfer in this page 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Is this 
atlas can be generated with the presence of FLAIR images.

When i run recon-all without FLAIR or T2 I don't see this atlas!! Is this atlas 
FLAIR -based?

thank you for any clarification
John

>  Original Message 
> Subject: aparc.DKTatlas+aseg.mgz
> Local Time: August 30, 2017 7:49 PM
> UTC Time: August 30, 2017 11:49 PM
> From: john.ande...@protonmail.com
> To: Freesurfer support list 
>
> Dear experts,
> looking into the output of Freesurfer in this page 
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
> I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Do I need 
> FLAIR images to get this file.
>
> I ran the command recon-all --s subj --all and I can';t find this file
>
> thank you for any clarification
> John___
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[Freesurfer] aparc.DKTatlas+aseg.mgz

[John Anderson]

Dear experts,
looking into the output of Freesurfer in this page 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Do I need 
FLAIR images to get this file.

I ran the command recon-all --s subj --all and I can';t find this file

thank you for any clarification
John___
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[Freesurfer] sub-cortical analysis

[John Anderson]

Hi Dr Greve,

I am using pet surfer to analyze suv images. I followed all the steps in wiki, 
I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm} into 
surface based analysis for left and right hemispheres. I want to inquire about 
the sub cortical analysis.

1. I assume the analysis for sub cortical gray matter (i.e. using the images 
subctxgm) is volumetric. Is this correct?

2. Are the following steps correct for sub cortical gray matter analysis

mri_vol2vol --mov subctxgm.nii.gz --reg reg.dat --tal --talres 2 --talxfm 
talairach.xfm --nearest --no-save-reg --o subctxgm.tal2mm.nii.gz

mri_mask subctxgm.tal2mm.nii.gz 
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz 
subctxgm.tal2mm_subc.nii.gz &

Concatenate all subjects together using mri_concat

smooth using mri_fwhm (what is the recommended smoothing for suv)?

 Then Group analysis:

mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C contrast.mtx 
--glmdir dir

mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166

 for "mri_glmfit-sim"  in subcortical structure is the flag grf  correct or 
cache?

Thanks in advance!
John___
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[Freesurfer] sub cortical analysis

[John Anderson]

Hi Dr Greve,

I am using pet surfer to analyze suv images. I followed all the steps in wiki, 
I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm} into 
surface based analysis for left and right hemispheres. I want to inquire about 
the sub cortical analysis.

1. I assume the analysis for sub cortical gray matter (i.e. using the images 
subctxgm) is volumetric. Correct?

2. Are the following steps correct for sub cortical gray matter analysis

mri_vol2vol --mov subctxgm.nii.gz --reg reg.dat --tal --talres 2 --talxfm 
talairach.xfm --nearest --no-save-reg --o subctxgm.tal2mm.nii.gz

mri_mask subctxgm.tal2mm.nii.gz 
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz 
subctxgm.tal2mm_subc.nii.gz &

Concatenate all subjects together using mri_concat

smooth using mri_fwhm (what is the recommended smoothing for suv)?

 Then Group analysis:

mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C contrast.mtx 
--glmdir dir

mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166

 for "mri_glmfit-sim"  in subcortical structure is the flag grf  correct or 
cache?

Thanks in advance!
John___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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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
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Re: [Freesurfer] mri_vol2surf

[John Anderson]

> Thank you for the response
>
> It is FDG SUV map
>
> need more info, eg, what kind of map is that? what modality?
>
>>  Original Message 
>> Subject: mri_vol2surf
>> Local Time: August 22, 2017 11:04 AM
>> UTC Time: August 22, 2017 3:04 PM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list 
>>
>> Dear FS experts,
>> I ran voxel-wise analysis between two groups using randomise in FSL and the 
>> final statistical maps is as attached.
>>  I aim to to repeat the analysis using surface based analysis. I followed 
>> the steps as in wiki. I am not sure what is the correct value for projfrac 
>> int he command "mri_vol2surf"  that is more appropriate to show the findings 
>> that I have in the voxel-wise (more int eh white matter) on surface.
>>
>> Thank you for any suggestion
>> John___
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