External Email - Use Caution
Dear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance.
Yours faithfully,
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up in an astonishing number of ways. By far the best thing to do would be to acquire a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to acquire one and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
External Email - Use CautionDear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance.
External Email - Use Caution
Hi Bruce,
I’ve talked to the MRI operator and she told me that the best thing to do the MP-RAGE protocol is doing the T1 weighted 3D gradient echo with SENSE, she can’t set the TE, TR, TI just like the ADNI protocol asked, though. She can set the thickness to 1 mm. Is this set up okay?
I have the DIACOM files of some subjects with the set up above. Can I send them to you to look at them?
I am terribly sorry for keep asking this basic question due to we never had experience doing it in Indonesia.
Many thanks!
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
On 2 Apr 2019, at 20.49, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up in an astonishing number of ways. By far the best thing to do would be to acquire a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to acquire one and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
External Email - Use CautionDear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mustafa, why not just run recon-all on the data you have and see whether it looks ok?
On 4/15/19 7:06 AM, mustafa amin wrote:
External Email - Use CautionHi Bruce,
I’ve talked to the MRI operator and she told me that the best thing to do the MP-RAGE protocol is doing the T1 weighted 3D gradient echo with SENSE, she can’t set the TE, TR, TI just like the ADNI protocol asked, though. She can set the thickness to 1 mm. Is this set up okay?
I have the DIACOM files of some subjects with the set up above. Can I send them to you to look at them?
I am terribly sorry for keep asking this basic question due to we never had experience doing it in Indonesia.
Many thanks!
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
On 2 Apr 2019, at 20.49, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up in an astonishing number of ways. By far the best thing to do would be to acquire a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to acquire one and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
External Email - Use CautionDear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Douglas, I tried to follow the instruction to recon-all the data however it didn't work. Please give some thoughts. Thank you in advance. Yours faithfully, Mustafa Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu menulis:
Hi Mustafa, why not just run recon-all on the data you have and see whether it looks ok?
On 4/15/19 7:06 AM, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
I’ve talked to the MRI operator and she told me that the best thing to do the MP-RAGE protocol is doing the T1 weighted 3D gradient echo with SENSE, she can’t set the TE, TR, TI just like the ADNI protocol asked, though. She can set the thickness to 1 mm. Is this set up okay?
I have the DIACOM files of some subjects with the set up above. Can I send them to you to look at them?
I am terribly sorry for keep asking this basic question due to we never had experience doing it in Indonesia.
Many thanks!
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
On 2 Apr 2019, at 20.49, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up in an astonishing number of ways. By far the best thing to do would be to acquire a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to acquire one and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
External Email - Use Caution
Dear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mustafa
can you give us some detials? What didn't work? Can you send us the full command line, screen output and recon-all.log?
cheers Bruce
On Thu, 16 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Douglas,
I tried to follow the instruction to recon-all the data however it didn't work. Please give some thoughts. Thank you in advance.
Yours faithfully,
Mustafa
Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu menulis:
Hi Mustafa, why not just run recon-all on the data you have and see whether it looks ok?
On 4/15/19 7:06 AM, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
I’ve talked to the MRI operator and she told me that the best thing to do the MP-RAGE
protocol is doing the T1 weighted 3D gradient echo with SENSE, she can’t set the TE, TR, TI just like the ADNI protocol asked, though. She can set the thickness to 1 mm. Is this set up okay?
I have the DIACOM files of some subjects with the set up above. Can I send them to you to
look at them?
I am terribly sorry for keep asking this basic question due to we never had experience
doing it in Indonesia.
Many thanks!
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
On 2 Apr 2019, at 20.49, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up in an astonishing number of ways. By far the best thing to do would be to acquire a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to acquire one and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
External Email - Use Caution
Dear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce,
Herewith I attach within the email the command that didn't work when I wanted to reconall. Please have a look. What about the previous dicom that I have sent to you? Please share some thoughts.Thank you very much.
Yours faithfully,
Mustafa
Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl fischl@nmr.mgh.harvard.edu menulis:
Hi Mustafa
can you give us some detials? What didn't work? Can you send us the full command line, screen output and recon-all.log?
cheers Bruce
On Thu, 16 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Douglas,
I tried to follow the instruction to recon-all the data however it didn't work. Please give some thoughts. Thank you in advance.
Yours faithfully,
Mustafa
Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu menulis:
Hi Mustafa, why not just run recon-all on the data you have and see whether it looks ok?
On 4/15/19 7:06 AM, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
I’ve talked to the MRI operator and she told me that the best thing to do the MP-RAGE
protocol is doing the T1 weighted 3D gradient echo with SENSE, she can’t set the TE, TR, TI just like the ADNI protocol asked, though. She can set the thickness to 1 mm. Is this set up okay?
I have the DIACOM files of some subjects with the set up above. Can I send them to you to
look at them?
I am terribly sorry for keep asking this basic question due to we never had experience
doing it in Indonesia.
Many thanks!
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
On 2 Apr 2019, at 20.49, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up in an astonishing number of ways. By far the best thing to do would be to acquire a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to acquire one and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
External Email - Use Caution
Dear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mustafa
1. Your mprage ran through recon-all fine and the results look good. The saggital field of view is tight, so make sure that they don't crop brain in that direction.
2. Your recon-all command line is incorrect. You should point the SUBJECTS_DIR environment variable to whereever you want to store all of your FreeSurfer-processed data, then use the -i switch to path to the input volume. You can also specify SUBJECTS_DIR on the command line. So in your case something like:
recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001 -sd \ /path/to/my/subjecs -all
should do the trick. There is also no need to convert to nifti first
cheers Bruce
On Fri, 17 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
Herewith I attach within the email the command that didn't work when I wanted to reconall. Please have a look. What about the previous dicom that I have sent to you? Please share some thoughts.Thank you very much.
Yours faithfully,
Mustafa
Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl fischl@nmr.mgh.harvard.edu menulis:
Hi Mustafa
can you give us some detials? What didn't work? Can you send us the full command line, screen output and recon-all.log?
cheers Bruce
On Thu, 16 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Douglas,
I tried to follow the instruction to recon-all the data however it didn't work. Please give some thoughts. Thank you in advance.
Yours faithfully,
Mustafa
Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu menulis:
Hi Mustafa, why not just run recon-all on the data you have and see whether it looks ok?
On 4/15/19 7:06 AM, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
I’ve talked to the MRI operator and she told me that the best thing to do the MP-RAGE
protocol is doing the T1 weighted 3D gradient echo with SENSE, she can’t set the TE, TR, TI just like the ADNI protocol asked, though. She can set the thickness to 1 mm. Is this set up okay?
I have the DIACOM files of some subjects with the set up above. Can I send them to you to
look at them?
I am terribly sorry for keep asking this basic question due to we never had experience
doing it in Indonesia.
Many thanks!
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
On 2 Apr 2019, at 20.49, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up in an astonishing number of ways. By far the best thing to do would be to acquire a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to acquire one and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
External Email - Use Caution
Dear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce,
Thank you for your swift response as always, may I know how to convert the more than 100 DICOM files to mgz or nifti? I noticed that the command is for 1 file/image, please correct me if I am wrong. The MP-RAGE file that I sent you is more than 50 images.
I tried to follow your instruction however it did not work smoothly. The diacom files couldn't be converted to mgz. I have attached the command that still did not work when I used them in this email. Please have a look and share some thoughts. Thank you for your kind attention and cooperation.
Pada Jumat, 17 Mei 2019 21.14.44 WIB, Bruce Fischl fischl@nmr.mgh.harvard.edu menulis:
Hi Mustafa
1. Your mprage ran through recon-all fine and the results look good. The saggital field of view is tight, so make sure that they don't crop brain in that direction.
2. Your recon-all command line is incorrect. You should point the SUBJECTS_DIR environment variable to whereever you want to store all of your FreeSurfer-processed data, then use the -i switch to path to the input volume. You can also specify SUBJECTS_DIR on the command line. So in your case something like:
recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001 -sd \ /path/to/my/subjecs -all
should do the trick. There is also no need to convert to nifti first
cheers Bruce
On Fri, 17 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
Herewith I attach within the email the command that didn't work when I wanted to reconall. Please have a look. What about the previous dicom that I have sent to you? Please share some thoughts.Thank you very much.
Yours faithfully,
Mustafa
Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl fischl@nmr.mgh.harvard.edu menulis:
Hi Mustafa
can you give us some detials? What didn't work? Can you send us the full command line, screen output and recon-all.log?
cheers Bruce
On Thu, 16 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Douglas,
I tried to follow the instruction to recon-all the data however it didn't work. Please give some thoughts. Thank you in advance.
Yours faithfully,
Mustafa
Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu menulis:
Hi Mustafa, why not just run recon-all on the data you have and see whether it looks ok?
On 4/15/19 7:06 AM, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
I’ve talked to the MRI operator and she told me that the best thing to do the MP-RAGE
protocol is doing the T1 weighted 3D gradient echo with SENSE, she can’t set the TE, TR, TI just like the ADNI protocol asked, though. She can set the thickness to 1 mm. Is this set up okay?
I have the DIACOM files of some subjects with the set up above. Can I send them to you to
look at them?
I am terribly sorry for keep asking this basic question due to we never had experience
doing it in Indonesia.
Many thanks!
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
On 2 Apr 2019, at 20.49, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up in an astonishing number of ways. By far the best thing to do would be to acquire a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to acquire one and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
External Email - Use Caution
Dear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mustafa
I believe I did:
mri_convert -it dicom IMAGE001 mprage.mgz recon-all -i mprage.mgz -sd <YOUR SUBJECTS DIR> -s <SUBJECT ID> -all
you can give it any *single* image in the correct series (don't give it more than one)
cheers Bruce
On Mon, 20 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
Thank you for your swift response as always, may I know how to convert the more than 100 DICOM files to mgz or nifti? I noticed that the command is for 1 file/image, please correct me if I am wrong. The MP-RAGE file that I sent you is more than 50 images.
I tried to follow your instruction however it did not work smoothly. The diacom files couldn't be converted to mgz. I have attached the command that still did not work when I used them in this email. Please have a look and share some thoughts. Thank you for your kind attention and cooperation.
Pada Jumat, 17 Mei 2019 21.14.44 WIB, Bruce Fischl fischl@nmr.mgh.harvard.edu menulis:
Hi Mustafa
- Your mprage ran through recon-all fine and the results look good. The
saggital field of view is tight, so make sure that they don't crop brain in that direction.
- Your recon-all command line is incorrect. You should point the
SUBJECTS_DIR environment variable to whereever you want to store all of your FreeSurfer-processed data, then use the -i switch to path to the input volume. You can also specify SUBJECTS_DIR on the command line. So in your case something like:
recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001 -sd \ /path/to/my/subjecs -all
should do the trick. There is also no need to convert to nifti first
cheers Bruce
On Fri, 17 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
Herewith I attach within the email the command that didn't work when I wanted to reconall. Please have a look. What about the previous dicom that I have sent to you? Please share some
thoughts.Thank
you very much.
Yours faithfully,
Mustafa
Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl fischl@nmr.mgh.harvard.edu menulis:
Hi Mustafa
can you give us some detials? What didn't work? Can you send us the full command line, screen output and recon-all.log?
cheers Bruce
On Thu, 16 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Douglas,
I tried to follow the instruction to recon-all the data however it didn't work. Please give some thoughts. Thank you in advance.
Yours faithfully,
Mustafa
Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu menulis:
Hi Mustafa, why not just run recon-all on the data you have and see whether it looks ok?
On 4/15/19 7:06 AM, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
I’ve talked to the MRI operator and she told me that the best thing to do the MP-RAGE
protocol is doing the T1 weighted 3D gradient echo with SENSE, she can’t set the TE, TR, TI just like the ADNI protocol asked, though. She can set the thickness to 1 mm. Is this set up okay?
I have the DIACOM files of some subjects with the set up above. Can I send them to you to
look at them?
I am terribly sorry for keep asking this basic question due to we never had experience
doing it in Indonesia.
Many thanks!
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
On 2 Apr 2019, at 20.49, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up in an astonishing number of ways. By far the best thing to do would be to acquire a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to acquire one and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
External Email - Use Caution
Dear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she had done the right protocol of MP-RAGE. I have attached the picture that has been taken by her. Please share some thoughts. Thank you in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Your attachment says that none of the commands could be found. Make sure you set up your environment correctly
On 5/20/19 4:53 AM, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
Thank you for your swift response as always, may I know how to convert the more than 100 DICOM files to mgz or nifti? I noticed that the command is for 1 file/image, please correct me if I am wrong. The MP-RAGE file that I sent you is more than 50 images.
I tried to follow your instruction however it did not work smoothly. The diacom files couldn't be converted to mgz. I have attached the command that still did not work when I used them in this email. Please have a look and share some thoughts. Thank you for your kind attention and cooperation.
Pada Jumat, 17 Mei 2019 21.14.44 WIB, Bruce Fischl fischl@nmr.mgh.harvard.edu menulis:
Hi Mustafa
- Your mprage ran through recon-all fine and the results look good. The
saggital field of view is tight, so make sure that they don't crop brain in that direction.
- Your recon-all command line is incorrect. You should point the
SUBJECTS_DIR environment variable to whereever you want to store all of your FreeSurfer-processed data, then use the -i switch to path to the input volume. You can also specify SUBJECTS_DIR on the command line. So in your case something like:
recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001 -sd \ /path/to/my/subjecs -all
should do the trick. There is also no need to convert to nifti first
cheers Bruce
On Fri, 17 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
Herewith I attach within the email the command that didn't work when
I wanted to reconall. Please
have a look. What about the previous dicom that I have sent to you?
Please share some thoughts.Thank
you very much.
Yours faithfully,
Mustafa
Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl
<fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> menulis:
Hi Mustafa
can you give us some detials? What didn't work? Can you send us the full command line, screen output and recon-all.log?
cheers Bruce
On Thu, 16 May 2019, mustafa amin wrote:
External Email - Use Caution
Hi Douglas,
I tried to follow the instruction to recon-all the data however it
didn't work. Please give
some thoughts. Thank you in advance.
Yours faithfully,
Mustafa
Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D.
<DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>
menulis:
Hi Mustafa, why not just run recon-all on the data you have and see whether it looks ok?
On 4/15/19 7:06 AM, mustafa amin wrote:
External Email - Use Caution
Hi Bruce,
I’ve talked to the MRI operator and she told me that the best
thing to do the MP-RAGE
protocol is doing the T1 weighted 3D gradient echo with SENSE, she
can’t set the TE, TR, TI
just like the ADNI protocol asked, though. She can set the
thickness to 1 mm. Is this set
up okay?
I have the DIACOM files of some subjects with the set up above.
Can I send them to you to
look at them?
I am terribly sorry for keep asking this basic question due to
we never had experience
doing it in Indonesia.
Many thanks!
Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
On 2 Apr 2019, at 20.49, Bruce Fischl
<fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Mustafa
MRI is an amazingly versatile technology that can be messed up
in an
astonishing number of ways. By far the best thing to do would
be to acquire
a dataset and run it through recon-all and see if the results look accurate. If you have permission to do so, you are welcome to
acquire one
and send it to us to try out instead.
cheers Bruce
On Tue, 2 Apr 2019, mustafa amin wrote:
External Email - Use Caution
Dear Freesurfer experts,
I need advice, the MRI operator need to confirm whether she
had done the
right protocol of MP-RAGE. I have attached the picture that
has been
taken by her. Please share some thoughts. Thank you in advance.
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-
Bruce Fischl -
Greve, Douglas N.,Ph.D. -
mustafa amin