[Freesurfer] a problem

Hi, experts, I am trying to use the template fsaverage_sym and tried to map the same set of vertices onto the left and right pial surface. Surprisingly, these vertices on the two surfaces did not correspond to the same anatomical cortical regions. Sometimes, they correspond to each other very

[Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

External Email - Use Caution Hi FreeSurfer Experts, I would like to do the surface analysis among two groups, like the thickness, volume and area. When I run the GLM, do I have to consider the eTIV as a covariant or not? Thanks a lot! Best wishes, Ting

Re: [Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

External Email - Use Caution Thank you so much! Ting > On Jun 29, 2018, at 2:10 PM, Douglas Greve wrote: > > Yes, for area and volume, no for thickness > > On 6/29/18 3:06 PM, Ting Li wrote: >> External Email - Use Caution >> >> Hi F

Re: [Freesurfer] convert nii to nii.gz

the environment variable FREESURFER_HOME is set > properly). If it is, you can do: > > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > Are you new to Linux also? If so, you might want to go through some basic > tutorials. > > cheers > Bruce > > On Fri, 19 Jan

[Freesurfer] Anatomical ROI analysis

Hi, all experts, I am studying the AnatomicalROIV6.0 tutorials. In the Anatomical ROI analysis tutorial, the first four part work well. While in the Group stats files, I got an error information like this. group_analysis_tutorial ting$ asegstats2table --subjects 004 021 040 067 080 092 \ >

[Freesurfer] Curvature Index and Folding Index

Dear FreeSurfer Expert, Could you explain me what does the curvature index and folding index mean in the Parcellation Stats File? In which way they are calculated? or you can give me some related documents. Thanks a lot. Ting ___ Freesurfer mailing

[Freesurfer] Does this analysis work for new born baby

Dear Stuff, Happy new year. Does Freesurfer work for new born baby MRI or not? If I want to use it for baby MRI, what should I pay attention to? Thanks a lot! Best wishes, Ting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Does this analysis work for new born baby

Thanks for your response. Ting > On Jan 3, 2018, at 9:48 AM, Lilla Zollei <lzol...@nmr.mgh.harvard.edu> wrote: > > > The currently available FS pipeline does not work for newborn infant brain > MRI. > Lilla > > On Tue, 2 Jan 2018, Ting Li wrote: > >

[Freesurfer] questions about the segamentation volume

Hi FreeSurfer Expert, I followed the Anatomical ROI analysis tutorial and make a aseg.vol.table for the 40 subjects. However, the segment volume can various a lot in different subjects, such as Left-Lateral-Ventricle, Left-Inf-Lat-Vent. I attached a screenshot. Thanks for your response. Best

Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Hi Douglas, You instruction works perfect. Thanks a lot. Regards, Ting > On Aug 14, 2018, at 11:01 AM, Ting Li wrote: > > Hi experts, > > I have a significant cortical thickness cluster and want the cluster > thickness in

Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Hi experts, How to create the stack of P2P3.stack.mgh after mris_preproc and mir_surf2surf? Great thanks. Regards, Ting > On Aug 14, 2018, at 10:51 AM, Douglas Greve wrote: > > First, run mris_preproc and mri_surf2surf commands as before to

Re: [Freesurfer] question about the GLM power

size(rstd.vol)).*rstd.vol; % add noise > fname = sprintf('synth%04d.mgh',n); > MRIwrite(y,fname); > end > > On 07/16/2018 01:43 PM, Ting Li wrote: >> External Email - Use Caution >> >> Hi Douglas, >> >> Thanks for your response. I did the mon

Re: [Freesurfer] question about the GLM power

eve wrote: > > I'm not sure what you mean by this. power with clusterwise corrections > is quite tricky. You'd have to do a simulation under non-null conditions > to see what the true positive rate is > > > > On 07/10/2018 11:53 AM, Ting Li wrote: >> Exter

Re: [Freesurfer] Multiple comparison - permutation

; > > On 07/05/2018 12:34 PM, Ting Li wrote: >> >> External Email - Use Caution >> >> Dear Freesurfer Experts, >> >> I am running the multiple comparison (permutation) on a MAC with the >> following code. It has taken 8 hours and ha

Re: [Freesurfer] Using a cluster as an ROI for further analysis

External Email - Use Caution Hi experts, I have extracted the area of the significant cluster with the command like the following: mri_segstats --i mgh/lh.volume.all.mgh --seg glmdir_az_vz/lh.volume.all.glmdir/av-group2-vs-group2/cache.th20.neg.sig.ocn.mgh --id 1 --sumwf

[Freesurfer] question about the GLM power

of the clusterwise correction results has disappeared. Can you help me on this? Thanks a lot! Best wishes, Ting Li ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

Re: [Freesurfer] glmfit-sim FWHM 34?

External Email - Use Caution Hi Douglas, I try to use permutation but it takes forever. I never see the end. Do I have to update the freesurfer to use the permutation? As it was recommended in this year? Best, Ting > On Jul 3, 2018, at 11:07 AM, Douglas N. Greve wrote: > >

[Freesurfer] convert nii to nii.gz

Hi Freesurfer Expert, I am very new to Freesurfer and have a very basic question. How to convert .nii files to nii.gz? I have tried the mri_convert subject_name.nii to subject_name.nii.gz directly. It gives me an error information that mri_convert: command not found. Thanks for your help!

Re: [Freesurfer] convert nii to nii.gz

l sysadmins? > > cheers > Bruce > On Sat, 20 Jan 2018, Ting Li wrote: > >> Hi Bruce, >> Thanks for your quickly response. Sorry for my late. >> I try to run FreeSurfer in a server. It was installed in my home share >> folder. Here is the setting >> envir

[Freesurfer] Recon-all with custom atlas

External Email - Use Caution Hi Freesurfer Experts, We want to run recon-all with a custom atlas which is generated from ANTs multivariate template construction. What is the right procedure to run recon-all? Run recon-all to my atlas itself first and them use this output as a

Re: [Freesurfer] Recon-all with custom atlas

las N. Greve <dgr...@mgh.harvard.edu> wrote: > > Is the atlas in GCA format? If so, then you can use gca-apply > > > On 04/19/2018 10:09 AM, Ting Li wrote: >> Hi Freesurfer Experts, >> >> We want to run recon-all with a custom atlas which is generated from

Re: [Freesurfer] Recon-all with custom atlas

subjects and perform the GLM analyses? I really need your help for this. Thanks for your time. Best, Ting > On Apr 19, 2018, at 11:42 AM, Ting Li <tx...@ualr.edu> wrote: > > Douglas, > > Thank you so much for your response. My atlas is nii.gz format. What should I >

Re: [Freesurfer] Recon-all with custom atlas

't need to have > an accurate volume template. If you want to use a custom volume-based > segmentation atlas, then you'll need to run gcatrain and gca-apply > > > On 04/19/2018 01:28 PM, Ting Li wrote: >> External Email - Use Caution >> >> Douglas, >>

Re: [Freesurfer] Recon-all with custom atlas

tes> ) is the right way to go? Thanks for your time. Best, Ting > On Apr 19, 2018, at 2:22 PM, Ting Li <tx...@ualr.edu> wrote: > > Douglas, > > Thanks for your quick response. If I only want the information of cortical > thickness, surface area, volume for va

Re: [Freesurfer] Recon-all with custom atlas

External Email - Use Caution Thanks for your patience with me. I am really appreciate. : ) Ting > On Apr 19, 2018, at 3:14 PM, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > > The wiki and the papers :) > > > On 04/19/2018 03:22 PM, Ting Li wrote: &

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

> Which subject did you load it on? It must be fsaverage. Can you send the > terminal output and command line? > > On 10/03/2018 11:31 PM, Ting Li wrote: >> >> External Email - Use Caution >> >> Dear Freesurfer Expert, >> >> I have f

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

the Annotation from the panel just below it. It does not make > sense that you would see the branches on the folded surface but not on > the inflated. > > On 10/15/2018 03:06 PM, Ting Li wrote: >> >> External Email - Use Caution >> >> I didn't load

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

lated surface, do you still see the branch? > > On 10/15/2018 08:42 PM, Ting Li wrote: >> External Email - Use Caution >> >> The annot file loaded successfully and without any branches. Thanks a lot. >> >> Ting >>> On Oct 15, 2018, at 2:22 PM, Greve

[Freesurfer] create label from cluster obtained with mri_glm-fit-sim

External Email - Use Caution Dear Freesurfer Experts, I really need your attention and help. Thanks a lot. We want to create label through the mri_glm-fit-sim cluster results. We have found the same topic in 2013 and tried the method you have provided. However, it doesn’t

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

External Email - Use Caution I have also tried the command without annot in specifying the annotation file. Thanks a lot. Regards, Ting > On Oct 3, 2018, at 9:36 PM, Ting Li wrote: > > Dear Freesurfer Experts, > > I really need your attention and help. Thanks

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

to create label through mri_glm-fit-sim clusters. What command I should use? Please specify it for me. Thanks a lot! Your help means a lot. Regards, Ting > On Oct 3, 2018, at 9:38 PM, Ting Li wrote: > > I have also tried the command without annot in specifying the annotation >

[Freesurfer] Set annotation cluster color

External Email - Use Caution Dear Freesurfer Expert, Can I change the color of loading from the annot file in Freeview? Thanks a lot! Best regards, Ting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] aparc.pial.stats

External Email - Use Caution Thank you so much! It is really helpful. Best regards, Ting Li > On May 9, 2019, at 3:15 PM, Greve, Douglas N.,Ph.D. > wrote: > > You can use aparcstats2table, just specify -p aparc.pial > > On 5/8/19 11:17 PM, Ting Li wrote: &

[Freesurfer] aparc.pial.stats

External Email - Use Caution Dear Freesurfer Expert, Is there a way to get the aparc.pial.stats in one command like aparcstats2table? Thanks a lot! Best regards, Ting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] White surface area and cortical surface area

External Email - Use Caution Dear Freesurfer Experts, I have a very simple question. The white surface area we extract from the ?h.aparc.stats is the same area we used in the mri_surf2surf by parameter area? or the mri_surf2surf is the pial surface area? I am looking forward to

Re: [Freesurfer] Multiple comparison using Monte Carlo

; Correct. This is no different than, eg, a t-test. Look in the back of a > stats book from the 1950s and you will find a table of t-ratios and > corresponding p-values. Obviously, they did not have access to any of the > data being analyzed today:), but the tables are still valid. > > On 12/2/201

Re: [Freesurfer] Multiple comparison using Monte Carlo

External Email - Use Caution Dear Dr. Douglas, Thank you so much! Best regards, Ting On Thu, Dec 5, 2019 at 11:45 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > I've attached a couple of papers > > On 12/3/19 9:24 PM, Ting Li wrote: > >

Re: [Freesurfer] Multiple comparison using Monte Carlo

PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > > > On 12/3/2019 1:36 PM, Ting Li wrote: > > External Email - Use Caution > Dear Dr. Douglas, > > Thank you so much for all the answers. I have two more questions. > > 1, When the Monte Car

Re: [Freesurfer] Multiple comparison using Monte Carlo

gt; wrote: > That will use the pre-computed ("cached") CSD files distributed with > FreeSurfer. This used 10,000 iterations. > > On 12/1/2019 11:34 PM, Ting Li wrote: > > External Email - Use Caution > Dear Freesurfer Expert: > > I have used the simulation code as

Re: [Freesurfer] Multiple comparison using Monte Carlo

with the analysis metrics that I have used. Do I understand correctly? Best regards, Ting Li On Mon, Dec 2, 2019 at 11:57 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > > > On 12/2/2019 11:58 AM, Ting Li wrote: > > External Email - Use Caution > Dear Dr

[Freesurfer] Multiple comparison using Monte Carlo

External Email - Use Caution Dear Freesurfer Expert: I have used the simulation code as show below: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces My question is how many iterations are done during this simulation? I didn’t

Re: [Freesurfer] Multiple comparison using Monte Carlo

a t-test. Look in the back of a > stats book from the 1950s and you will find a table of t-ratios and > corresponding p-values. Obviously, they did not have access to any of the > data being analyzed today:), but the tables are still valid. > > On 12/2/2019 2:03 PM, Ting Li wrote: &g

[Freesurfer] cortical area and volume calculation method

External Email - Use Caution Dear Freesurfer Experts, Where I can find any document that explaining how the cortical area and volume were calculated? or Could you give me an introduction about it. Thank you so much! Best regards, Ting